A long-awaited deal between Gov. Andrew M. Cuomo and New York City Mayor Bill de Blasio will ensure $26.1 billion in MTA transportation infrastructure projects can go forward, including the completion of East Side Access and the construction of a second LIRR track between Farmingdale and Ronkonkoma, officials said Saturday.

The agreement to fund the MTA's five-year capital program comes later in the budget process than any time during its 32-year history, and just weeks before the Metropolitan Transportation Authority said it would run out of money to award key construction contracts for East Side Access -- potentially further pushing back the delay-plagued megaproject.

"This plan will mean a safer, stronger, more reliable transit system for people all over New York, and is crucial in supporting our growing economy. And this program would not have been possible without everyone stepping up to pay their fair share," Cuomo said in a statement.

The plan, proposed by the MTA more than a year ago, includes $2.8 billion to complete East Side Access, which promises to link the Long Island Rail Road to Grand Central Terminal by 2022; $250 million to complete the LIRR Double Track project in Suffolk; $465 million to buy 164 new M9 electric LIRR cars to replace the 30-year-old M3 fleet; $196 million to finish installation of positive train control crash-prevention systems on the LIRR and Metro-North; and $40 million to build an LIRR station in Elmhurst.

In July, the MTA and Cuomo proposed a plan to fund the program with $17 billion generated by the authority, $8.3 billion in state aid and $3.2 billion from the city. But de Blasio's administration, which had been offering to contribute $657 million to the capital plan, balked at the request, arguing that the city already pays more than its fair share, including $1 billion annually for the MTA's operating budget.

The MTA countered that New York City's capital contribution had hardly changed in three decades, even though the primary mission of the public transportation agency -- the largest in North America -- is transportation within and to and from the city.

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Cuomo and MTA chairman Thomas Prendergast publicly called out de Blasio repeatedly over the last two months for holding up the plan, and de Blasio, who has been feuding with Cuomo on several fronts, returned the sniping.

A source close to the process said in-person talks involving city, state and MTA principals and staffers went on for weeks, and that a deal appeared within reach earlier this past week. "At various times, it seemed like the deal was on and at various times it seemed like the deal was totally off," the source said.

The mayor finally agreed to kick in $2.5 billion with the assurance that his administration will have a hand in planning projects in the city "with priority given for projects and timing based on input from the city," according to the agreement. Suburban projects, including those on Long Island, will similarly be coordinated with local officials.

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A statement from de Blasio said the city was making "its largest-ever general capital contribution -- while ensuring that NYC dollars stay in NYC transit, and giving NYC riders and taxpayers a stronger voice." He added, "I look forward to continuing to partner with the governor and the MTA to ensure a transit system that reliably, effectively, and safely serves all of its riders."

Prendergast said the agency has "plenty of work to do and we're eager to get started."

"Today, with agreement on the largest capital program ever committed to the future of the MTA, we take a giant step toward making sure that this one-of-a-kind jewel of a system will continue doing what it must -- keeping New York and the region moving, and moving ahead," his statement said.

Because the city's promised contribution is $700 million short of what the MTA earlier sought, the agency will be forced to find efficiencies, including possibly scaling back the program. But spokesman Adam Lisberg said the MTA is "confident" that it could come up with savings so the plan can be kept intact.

The full MTA board will vote on a revised program on Oct. 28. If passed, the program will be sent to the five-member MTA Capital Program Review Board for final approval.

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Few details have emerged on how the MTA, state and city plan to cover the massive cost. The MTA has said it will cover most of its share by issuing bonds backed by revenue from its payroll mobility tax. New York City will cover $1.9 billion from "direct city sources" and the other $600 million through "alternative, non-tax levy revenue." The state's share will come from its general fund.

As part of the deal, the state and city promised not to divert any funds committed to the MTA for any other expenses.

The agreement won praise from unions and rider advocates. The LIRR's chief union leader, Anthony Simon, praised Cuomo for "spearheading the largest effort in history to keep the MTA running safely."

"Public transportation ridership is growing throughout the region, and since the most intense pressure is felt in the city where 90 percent of the MTA's customers are, it's only fair that the city help pay to keep the subways and buses moving," said Simon, general chairman of the Sheet Metal, Air, Rail and Transportation Union.

The MTA's biggest union, the Transport Workers Union Local 100, similarly credited Cuomo for securing "a great win" for transit workers and passengers.

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Transit advocacy groups, including the Straphangers Campaign, Tri-State Transportation Campaign, Transportation Alternatives and Pratt Center for Community Development, called the deal "good news" and the promised $26.1 billion a significant shot in the arm for "a transit system that has suffered from decades of underinvestment by the city and state."