The Metropolitan Transportation Authority nailed down $2.6 billion in federal funds yesterday to build a network of tunnels connecting the Long Island Rail Road to Grand Central Terminal, clearing the way for national and local leaders to renew a call for the JFK rail link.

The U.S. transportation secretary, Mary Peters, signed over the funds during a news conference at Grand Central Terminal yesterday. They will pay for 40% of the East Side Access project, as well as $693 million to fund an early phase of construction on the Second Avenue subway line.

Senator Schumer applauded the development. “We in the New York congressional delegation don’t have to spend all our time putting money into this project, allowing us to turn our focus to others,” such as the JFK rail link, he said.

The JFK rail link has long been supported by business leaders who are seeking to reinvigorate downtown, but critics say they think the project is too expensive and a waste of resources.

Mr. Schumer said $2 billion of the $20 billion of tax credits earmarked for Lower Manhattan development after the September 11 attacks would be put toward the connection between Lower Manhattan and JFK airport within the first six months of the new congressional term. Congress rejected the funding for the project earlier this year.

Governor Pataki, a long-time proponent of the JFK rail link, said yesterday that he felt “confident that we’ll get additional federal help so that the train to the plane from Lower Manhattan to JFK can become a reality.”

Governor-elect Spitzer has made it clear that the JFK rail link is not one of his priorities, and that the construction of the Second Avenue subway line and the East Side Access project are better investments for the city.

Another opponent is Rep. Jerrold Nadler. “The JFK railway link is a project that the congressman does not think highly of at all,” a spokesman for the congressman, Robert Gottheim, said. “Do we need a third one-seat ride when you can get there with East Side Access?”

Mr. Nadler has also expressed concern about spending money on an expensive project before the required Environmental Impact Statement has been completed.

The agreement signed yesterday, which virtually guarantees the completion of the East Side Access project, also provides leverage for New York’s congressional leaders to look for more funding sources from Congress.

The MTA expects to receive a grant of $1.3 billion in 2008 to fund further construction.

The connection between the LIRR and Grand Central Terminal is expected to encourage many drivers from Long Island to switch to mass transit, and will cut an estimated 40 minutes from the daily commutes for the tens of thousands of passengers who use the railroad and work on the East Side. The project is slated for completion in 2013.

Mr. Schumer also spoke yesterday of connecting Stewart Airport to the city’s mass transit system to help relieve congestion at the three terminal airports in the region.

Ms. Peters also noted that the Federal Transit Administration is providing $4.5 billion to help fund the Fulton Street Transit Center and the connecting PATH terminal. The Fulton Street Transit Center, which links a dozen subway lines, is fully funded by federal money the city received to rebuild Lower Manhattan after the attacks of September 11. The project’s cost has risen to $844 million, which is $50 million over budget, and the original plans for the project have been scaled back to avoid more cost overruns, which will have to be paid for out of the MTA’s pocket.