The MTA has enough money to fund $17 billion of the plan using an additional $2.4 billion from unexpected revenues and cost-cutting measures. That means the capital projects budget gap is now $9.8 billion, down from $14 billion.
MTA Chairman Tom Prendergast wrote in a letter to city and state officials that the city should contribute an additional $200 million per year over five years in addition to the city's already increased base contributions of $657 million over five years.
The MTA also wants the city to cover the non-federal share of the $1.5 billion costs to launch the next phase of the badly needed Second Avenue Subway.
The city would contribute a total cost of $3.2 billion while the state would kick in $8.3 billion.
"City funding of the MTA’s operating and capital finance needs has been seriously deficient for many years despite the fact that more than 90 percent of the MTA’s daily customers are on MTA New York City Transit subway and bus services, and 80 percent of the MTA’s physical infrastructure is in New York City," Prendergast wrote in the letter.
Speaking on NY1 Thursday, Cuomo, who controls the MTA, backed the proposal.
"Historically, the city didn’t fund the MTA proportionately. That’s because, historically, the city was broke," Cuomo said.
"New York City is a lion share of the riders. They’re a lion share of the assets and I understand they haven’t paid much historically, but the city’s financial condition is much different than it was," Cuomo added.
City officials said they would be willing to work with the MTA but expressed concern over its math.
In a letter to Prendergast, Deputy Mayor Anthony Shorris said the city already increased its capital contribution to $657 million to match the MTA's request earlier this year. In addition, the city already contributes 70 percent of the MTA's operating budget through fares, tolls and taxes.
In the 2014 fiscal year, the MTA operating budget was $13.9 billion but city residents paid $10.1 billion in fares, tolls and taxes. That figure is $288 million more than the MTA spent on buses and subways in the five boroughs, say city officials.
The funding buys the city very little control.
"Although New York City residents contribute the vast bulk of its revenues through fares, tolls, and taxes, the city has relatively little say over the agency and its operating and capital priorities," Shorris wrote.
A recent report from Comptroller Scott Stringer's office found that each city household pays an "invisible fare" of $130 to subsidize the MTA before buying a MetroCard or paying a toll through taxes and other city subsidies for the agency.
In addition, federal funding of the MTA would have to increase $1.6 billion to $4.6 billion to match past support.
De Blasio spokeswoman Amy Spitalnick said the city was looking "forward to understanding the source of the additional State funding" and applauded Cuomo's "commitment to — for the first time — start to address the chronic underfunding" of the MTA.
“We are reviewing the letter and...are ready and willing to have a comprehensive conversation on a sustainable funding stream for the MTA," she added.
Nick Sifuentes, deputy director of the Riders Alliance, said the group hopes MTA cuts to its capital budget does not stop the improvements that most impact riders such as the continued expansion of communications-based train control which allow more trains to run closer together.
The proposed $8 billion contribution from the state should not entail the MTA taking on more debt which could translate into fare increases, he added.
"The state controls the MTA so the state needs to step up," said Sifuentes, "Should the city contribute more? Yes. But it's a little crazy to ask for $3.2 billion which is more than they've ever contributed before."
The disagreement between the city and the state over how to fund the MTA's capital plan comes as the agency's subway ridership is exploding. Last year, 1.75 billion straphangers rode the rails, a 2.6 percent increase.
At the same time, old equipment, mechanical failures, busted rails and signals and overcrowding has led to increased delays with more than 20 percent of all trains arriving late.
Both the city and state agree on one thing: Fares should not be increased beyond what is already planned to pay for the capital projects.
"Over-burdened riders" can't be expected to dig "even deeper into their pockets," Shorris said.
"I don’t think we should go to the riders and ask for an additional fare increase," the governor said on NY1. "I think that would be a mistake."