First the Gothamist article is from Oct. 2017. And you leave out the author's question mark from the end of her title.And she has a question mark for a reason, because This morning the B and Q were messed up, so I had to take three trains to work, two of which turned into other trains while I was on them

Second, I actually downloaded the 28-page report at the link, the link tells you nothing

I looked over the report..

Their rating of the cities is for Sustainable Urban Mobility.

It is not just about subways or even just about mass transit. It's about mobility, factoring nearly everything in, including geography and the urban plan.. I think it must include things like::cars and highways!, And airports! It does! It is not at all what you nor the Gothamist author present it to be.

They have used 3 factors

The People sub-index rates safety (traffic fatalities), access to transport services, share of trips taken by public transport, rider connectivity, digitization of the transport system, upkeep of the transport system, uptake of active commuting, airport passengers, hours of metro accessibility and wheelchair access. These indicators can broadly be thought of as capturing “quality of life” for a city’s commuters and visitors.

The Planet sub-index ranks cities on greenhouse gas emissions, congestion and delays, efforts to lower transport emissions, bicycle infrastructure, air pollution, provision of green space and electric vehicle incentives. These indicators can be broadly thought of as “green factors".

.The Profit sub-index examines commuting travel time in a city, transport revenues as a share of expenses, public finance commitment, affordability of public transport, system utilization and efficiency of road networks. These indicators can broadly be thought of as capturing “economic health”.

3.3 OVERALL INDEX RANKINGS The overall Index rankings reveal some key trends. Firstly, Europe dominates the top of the Index. Of the top ten places, seven are taken by European cities. Many of these European cities benefit from established and well-used metro networks such as London’s Underground, strong bicycle infrastructure in cities like Amsterdam and Copenhagen, and high shares of commuters using public rather than private transport. European cities are also environmentally conscious, with incentives to lower emissions reflected in cleaner air and greener mobility systems. Cities such as Zurich, Paris and 18 other European cities reflect these characteristics and sit in the top quartile of the Planet sub-index. Yet, the top spot in the Sustainable Cities Mobility Index is occupied by Hong Kong. The Asian city’s mobility system, underpinned by a wellorganized, modern and efficiently funded metro system, manages to achieve many of the aims of an effective urban transport system – enabling comprehensive mobility around a city, creating economic opportunity and enriching the lives of citizens, business and tourists alike. Two other Asian cities are in the top ten of the overall Index: Seoul and Singapore rank fourth and eighth, respectively. North American cities are spread throughout the overall Index, ranging from New York in 23rd place to Indianapolis in 88th. While citizens of some American cities enjoy well-funded and comprehensive transport systems, many cities in the U.S. and Canada are undermined by a reliance on private vehicles and underdeveloped public transport options. Most Australian cities sit in around the middle of the overall Index. A lack of comprehensive underground metro systems and dependence on private vehicles deters mobility in Australian cities, and all have less travel made by foot, bike and public transport than their peer cities. Greater utilization of urban public transport would improve mobility in cities like Perth and Canberra. Promisingly, underground train networks are being expanded in Sydney and Melbourne, and under consideration in Brisbane. South American and African cities sit lower in the overall Index. Cities like Rio de Janeiro, Buenos Aires and Santiago are hampered by congested roads and relatively low commitment to infrastructure spending. Cities such as Cairo still has some way to go in providing infrastructure for a popular and well-used mobility system. The research examines further the three sub-indices to see in which dimensions of sustainability cities are performing well in mobility and in which areas they have opportunities to boost investment and improve quality of life

These are the cities included:

d Undisclosed Undisclosed Undisclosed Hanoi Kuala Lumpur Cairo Undisclosed Bangkok Undisclosed Lima Jakarta Indianapolis Perth Houston Tampa Johannesburg Undisclosed Kolkata Detroit Denver Dallas Atlanta Pittsburgh Buenos Aires Mumbai Seattle New Orleans Los Angeles Istanbul Tianjin Undisclosed Wuhan Mexico City Cape Town San Diego Santiago Rio de Janeiro Manila Baltimore New Delhi Leeds Moscow Philadelphia Bengaluru Melbourne Toronto Canberra Miami Sydney Chengdu Chicago Brisbane São Paulo Boston Antwerp Dublin Bristol Washington DC Athens Rome Macau Birmingham Brussels Montreal Manchester Chennai Guangzhou Lisbon Geneva Taipei Warsaw Vancouver Shanghai San Francisco Rotterdam Madrid New York Berlin Barcelona Hamburg Shenzhen Milan Edinburgh Beijing Lyon Munich Tokyo Copenhagen Amsterdam Frankfurt Stockholm Singapore London Vienna Prague Seoul Paris Zurich H
 

I found this page on New York

NEW YORK New York City has some of the most intricate transportation networks in the U.S. and they are increasingly under strain from an expanding population, limited space, aging infrastructure and a booming economy. Key to preserving the lifeblood of New York is its connection to New Jersey, from which 400,000 residents commute into Manhattan daily to work, making transit efficiency between the two an imperative. The Port Authority of New York and New Jersey has so far had an eventful 2017, undertaking two major airport projects. Newark Liberty International Airport broke ground on the $2.4 billion renovation of Terminal A, a project that will include new bridges, a car park and interior modernization to accommodate more passengers. Improvements to LaGuardia Airport are also underway, including a $4 billion unified terminals program, which will update insufficient facilities and provide greater capacity to meet record-breaking passenger volumes. The Authority also approved a $32.2 billion capital plan at the beginning of the year for bus terminal improvements, as part of a ten-year infrastructure strategy. An affordable ferry service launched this year. In the future, New York is planning additional programs, such as the Gateway Program, to increase track, tunnel, bridge and station capacity between Newark, New Jersey and Penn Station, New York, a key economic corridor through which New Jersey residents commute to and from the city. Even with these improvements, New York is still faced with major challenges to ensure its infrastructure reaches the necessary levels. A continued focus on design-build, private finance and technology are all vital for the future. For instance, the Metropolitan Transportation Authority (MTA) is implementing an enterprise asset management program to optimize asset data tracking for lower operational costs, while enhancing safety and reliability. New York leads North America in the Index. But it is also a city with a lot to lose if its planned major infrastructure projects are postponed. 

 I note this line in the above SOUNDS VERY "NEO-LIBERAL" TO ME!

A continued focus on design-build, private finance and technology are all vital for the future 

Simplistic agitprop just really doesn't apply to NYC transit, Hal, it just doesn't. First of all, it's not under the state or local government, it's run by a huge entity that actually involves three states and funds for the highways and bridges and all the other rail services are in it. This is no doubt why it rates decently on that report. The area had a dense population a 100 yrs. ago. The running of NY State is a constant situation of robbing Peter to pay Paul with lots of corruption going on and few alive are capable of understanding how the heck it all even works.

All I know is we got a brand spanking new gorgeous Tappan Zee Bridge across the Hudson in Westchester Country built in like record time collecting $5 tolls each way but 3 airports that are described by all and sundry as third world quality (near rioting at JFK over rotten logistics during a storm was halted not by police but by the terminal being flooded from broken water pipes) are supposed to be in the process of being fixed but the horror just drags on and on and YES, a subway system that is in terrible danger of falling apart because they have neglected maintaining anything in order to: do things like:build the Tappan Zee Bridge! Just like the NYTimes says, they have neglected it, it's true, they have not been taking care of it and we are having big big troubles all the time over the last year.

Seems to me what they have been doing instead is to install automatic toll cameras everywhere, to collect more and more money (George Washington Bridge now: $15!) and have hired a private company to use those and other new cameras to send drivers automatic $50 tickets" when they go over 5 miles an hour going through the toll booth or go over 25 mph anywhere in the city. The amounts of money they take in grows and grows and grows and hardly anything seems to get done except more efficient ways of getting more money from users. So they don't have to raise taxes higher and higher, they just create more and new fees for everyone to pay.

Metropolitan Transportation Authority

The Metropolitan Transportation Authority (MTA) provides local and express bus, subway, and regional rail service in Greater New York, and operates multiple toll bridges and tunnels in New York City.

OverviewLocaleNew York City
Long Island
Lower Hudson Valley
Coastal ConnecticutTransit typeCommuter rail, local and express bus, subway, bus rapid transitNumber of lines

• 16 commuter rail routes
  • 5 Metro-North routes
  • 11 LIRR routes
• 26 rapid transit routes
  • 25 subway routes
  • 1 Staten Island Railway route
• 322 bus routes
  • 234 local routes
  • 71 express routes
  • 17 Select Bus Service routes

Daily ridership8,764,983 (weekday; all modes)Chief executiveVeronique Hakim
(Managing Director)[1]Headquarters2 Broadway, New York, NY 10004Websitemta.infoOperationBegan operation1965Operator(s)

• MTA Long Island Rail Road
• MTA Metro-North Railroad
• MTA New York City Subway
• MTA Regional Bus Operations
  • MTA Bus
  • MTA New York City Bus
• MTA Staten Island Railway

The Metropolitan Transportation Authority (MTA) is a public benefit corporation responsible for public transportation in the U.S. state of New York, serving 12 counties in Downstate New York, along with two counties in southwestern Connecticut under contract to the Connecticut Department of Transportation, carrying over 11 million passengers on an average weekday systemwide, and over 800,000 vehicles on its seven toll bridges and two tunnels per weekday. MTA is the largest public transit authority in the United States [....]

Here's the problem, short version: CORRUPTION AND/OR MIS MANAGEMENT AND BUREUCRACY. I can't bear reading it, most New Yorkers can't bear reading it either, it's just too complex and been happening far too long:

Expenses[edit]

Budget gaps[edit]

The budget deficit of the MTA is a growing crisis for the organization as well as for New York City and State residents and governments. The MTA held $31 billion in debt in 2010 and it also suffered from a $900 million gap in its operating budget for 2011.[88] The capital budget, which covers repairs, technological upgrades, new trains, and expansions, is currently $15 billion short of what the MTA states it needs. If this is not funded, the MTA will fund the repairs with debt and raise fares to cover repayments.

The MTA has consistently run on a deficit, but increased spending in 2000–04 coupled with the economic downturn led to a severe increase in the financial burden that the MTA bore. The budget problems stem from multiple sources. The MTA cannot be supported solely by rider fares and road tolls. In the preliminary 2011 budget, MTA forecasted operating revenue totaled at $6.5 billion, amount to only 50% of the $13 billion operating expenses.[89] Therefore, the MTA must rely on other sources of funding to remain operational. Revenue collected from real estate taxes for transportation purposes helped to contain the deficit. However, due to the weak economy and unstable real estate market, money from these taxes severely decreased; in 2010, tax revenue fell at least 20% short of the projected value.[90] Beyond this, steadily reducing support from city and state governments led to borrowing money by issuing bonds, which contributed heavily to the debt.[91]

This budget deficit has resulted in various problems, mainly concentrated in New York City. New York City Subway fares have been increased four times since 2008, with the most recent occurring March 22, 2015, raising single-ride fares from $2.50 to $2.75, express service from $6 to $6.50 and the monthly MetroCard fare from $112 to $116.[92] Each fare raise was met with increasing resistance by MTA customers, and many are beginning to find the fare increases prohibitive. 2010 also saw heavy service cuts for many MTA subsidiaries.[93] Fewer trains spaced farther between resulted in heavy overcrowding beyond normal rush hours, leading to frustration for many subway and bus riders.[94][95][96] In 2013, the subway had the highest ridership since 1947.[97] MTA employees also suffered due to the budget issues. By mid-July 2010, MTA layoffs had reached over 1,000, and many of those affected were low-level employees who made less than $55,000 annually.[98]

As of 2015, the MTA was running a $15 billion deficit in its $32 billion 2015–2019 Capital Plan.[99] Without extra funding, many necessary construction and renovation projects would not be performed.[100] In October 2015, the MTA passed the $29 billion 2015–2019 Capital Plan,[101] the largest capital plan in MTA's history; it will be funded by federal, state and city government as well as riders' fares and tolls.[102] Three months later, New York Governor Andrew Cuomo and MTA chairman Thomas Prendergast unveiled their plan to spend $26 billion to modernize the subway network, which includes adding Wi-Fi and cellphone services throughout all 278 underground stations by the end of 2016. Other plans call for making extensive renovations to 30 subway stations, allowing mobile ticketing by cellphone or bank cards, and adding security cameras on buses, charging stations for electronics, and more countdown clocks. Roughly $3 billion will be spent to improve bridges and tunnels.[103][104]

Reasons for high costs[edit]

On November 18, 2017, The New York Times published an investigation into the problems underlying the MTA. It found that politicians from both the Democratic and Republicanparties, at the mayoral and gubernatorial levels, had gradually removed $1.5 billion of MTA funding. Other actions by city and state politicians, according to the Times, included overspending; overpaying unions and interest groups; advertising superficial improvement projects while ignoring more important infrastructure; and agreeing to high-interest loans that would have been unnecessary without their other interventions.[105] The Times stressed that no single event directly caused the crisis; rather, it was an accumulation of small cutbacks and maintenance deferments.[106] The MTA funds were described as a "piggy bank" for the state, with the issuance of MTA bonds benefiting the state at the MTA's expense.[105] By 2017, a sixth of the MTA's budget was allocated to paying off debt, a threefold increase from the proportion in 1997. The city's $250 million annual contribution to the MTA budget in 2017 was a quarter of the contribution in 1990. David L. Gunn, who helped end a transit crisis when he led the NYCTA in the mid-1980s, described the 2017 crisis as "heartbreaking".[105]

In December of the same year, the Times reported that the $12 billion East Side Access project, which would extend the LIRR to Grand Central Terminal upon its completion, was the most expensive of its kind in the world, with a projected price of $3.5 billion per mile of track. Over the years, the projected cost of East Side Access had risen by billions of dollars due to unnecessary expenses. In addition to overpaying workers and overspending, politicians and trade unions had forced the MTA to hire more workers than was needed. In 2010, an accountant found that the project was hiring 200 extra workers, at a cost of $1,000 per worker per day, for no apparent reason. The bidding process for MTA construction contracts also raised costs because, in some cases, only one or two contractors would bid on a project. Similar construction projects in New York City, such as the Second Avenue Subwayand 7 Subway Extension, had been more expensive than comparable projects elsewhere for the same reasons, even though other cities' transit systems faced similar, or greater, problems compared to the MTA.[107]

Where one can usually find the truth about NYC mass transit, if one really needs it: from the most passionate users, not from the government nor for-profit consultancies. Thankfully, they too are a "lobbyist" but not as powerful as some others:

https://www.straphangers.org/issues/

Getting New York’s Subways Back on Track

Aging infrastructure and antiquated technology have contributed largely to the biggest issues plaguing our subway system. Recently, New York’s subway system has seen a major decline in service, with a steady increase of subway car breakdowns, subway cars that are filled beyond capacity with riders, and delays that have more than doubled in the past five years alone.

For several years, the Metropolitan Transportation Authority (MTA) has reassured riders it was prioritizing capital funds to move the system to a “state of good repair.” The MTA says it was caught flat-footed by the widespread problems in 2017, but in fact, it took specific steps that brought the system to its current state of disrepair. For example, transit managers have reduced standard maintenance cycles on subway cars. The MTA has also not replaced C train cars, which, at 45 years, have gone well past their useful life; as a result, they break down more regularly than any line in the system.

New York City’s subway system has suffered from both financial divestment and political neglect. The Straphangers Campaign will continue to advocate that the MTA prioritize funding projects that will return the subway system to a state of good repair.

Reimagining New York City’s Buses [....]