Aiming to win support for his anti-traffic tax from Governor Spitzer and Assembly Speaker Sheldon Silver, Mayor Bloomberg may agree to finance a larger portion of the Second Avenue Subway and scrap his plans to fund the JFK Rail Link.

In direct negotiations between Messrs. Bloomberg and Spitzer, as well as a series of discussions between city and state officials over the past week intended to hammer out a bill on congestion pricing before Memorial Day, talk has turned to omitting some transit improvements that were included in the city’s original 2030 plan, according to multiple sources close to the negotiations.

The $3.75 billion that was earmarked in the city’s sustainability plan for a rail link that would provide a direct connection between Lower Manhattan and John F. Kennedy International Airport, instead could help pay for the completion of the Second Avenue Subway, currently under construction but not yet fully funded.

The rail link has been a low-priority project for the executive director and CEO of the Metropolitan Transportation Authority, Elliot Sander, and the funding swap could warm him to Mr. Bloomberg’s plan, sources said. The East Side subway line, which would serve Mr. Silver’s district in Lower Manhattan if completed, has long been one of the speaker’s favored projects, as well as a priority for Mr. Spitzer.

Backing from state lawmakers and the MTA would strengthen New York’s chances of receiving federal funding for a three-year congestion pricing pilot program, where cars entering Manhattan South of 86th Street would pay $8 during peak hours, and trucks would pay $21. Under the current iteration of Mr. Bloomberg’s plan, those fees would be offset by any tolls paid to enter the city.

Transit advocates welcomed the prospect that more funds would be steered toward the East Side subway line. “The city needs a full length Second Avenue Subway, as opposed to the money being spread out in smaller pieces of big projects,” the chief attorney for the Straphangers Campaign, Gene Russianoff, said. “The problem over the last 10 years has been that if you’re for all of the projects, you’re really for none of them. That’s why they’ve inched along.”

Critics of the JFK Rail Link, which have included the Regional Plan Association, say the project would benefit fewer riders than a new subway line. Because it would cut down on the commute between Long Island’s North Shore and Lower Manhattan, some say it would mostly benefit downtown developers by narrowing the large gap between Midtown and Downtown rents.

“The JFK Rail Link was another $6 billion item that was always a boondoggle for downtown,” the executive director of New York Civic, Henry Stern, said.

The first segment of the Second Avenue Subway line would run between East 96th and East 63rd Streets and is expected to be completed by 2013. But the MTA has not yet secured funding to extend the line, to be known as the “T,” its full proposed length to Lower Manhattan. Deputy Mayor Daniel Doctoroff has repeatedly voiced his concerns over how that line would be completed.

The city’s plan would create a transit funding authority, known as the SMART fund, that would direct dollars raised through congestion pricing, as well as a commitment of city and state dollars, to help pay for the subway’s full construction, as well as other expansions to the system.

Mr. Sander on Friday expressed grave misgivings about the creation of a new funding authority at an oversight hearing run by Assemblyman Richard Brodsky, a Democrat of Westchester.

Mr. Silver’s tactic of waiting until the last moment to play his powerful card in the State Assembly has become his trademark negotiating style. He waited until after Governor Pataki and Mr. Bloomberg announced plans to spend $800 million on projects in Lower Manhattan before killing the city’s plan to build a stadium for the Jets on Manhattan’s West Side. He also rejected Mr. Pataki’s $900 million plan to build Moynihan Station, which could be revived now that Mr. Spitzer is in office.

In this case, Mr. Silver may be willing to give up one project he has favored in the past — the rail link — in order to get more money for a project he favors even more.

“Silver gets what he wants, but he’s also making a concession, because he wanted the rail link too,” Mr. Stern said. “There’s a price for everything he does, and sometimes the price is in the public interest.”

A spokesman for Mr. Silver, James Quent, said yesterday that Mr. Silver had not yet seen an official proposal promising more money for the Second Avenue Subway. A draft bill has been circulating among legislators for the past few weeks, sources said.

The Senate majority leader, Joseph Bruno, a Republican, has greeted Mr. Bloomberg’s plan more enthusiastically than Mr. Silver. He called the mayor’s presentation last week to Senate Republicans “outstanding,” and sources say he is likely to support the mayor’s plan.

Some of the other transit improvements that would be paid for with the fees levied from the proposed road tax would be the renovation of Pennsylvania and Moynihan stations, expanded ferry service, express bus lanes, as well as the construction of the no. 7 line.

Residential parking permits in the neighborhoods surrounding the tolled zone of Manhattan have been added to the plan, according to a source close to the negotiations. The city is still reviewing how it plans to issue and regulate government parking placards, and the treatment of trucks is still under discussion.