Therefore, “plaintiffs are entitled to be paid ‘just compensation’ by the city for the value” of the air rights, the lawsuit stated.

But SL Green and city officials pointed out that the developer had to commit to approximately $220 million in improvements to the crowded subway platforms and stairwells below Grand Central in exchange for the right to build the oversized tower. Construction of the tower, known as 1 Vanderbilt, has yet to start.

Jonathan Rosen, a spokesman for SL Green, said the project would not be “sidetracked by frivolous litigation.”

One Vanderbilt has received broad support within the city, Mr. Rosen said, “because of the project’s unprecedented commitment to improving the commutes for millions of New Yorkers and bringing state of the art office space to East Midtown.”

City officials declined to comment on the suit because they had not seen it. But Wiley Norvell, a spokesman for the mayor, said the rezoning and project were “critical” to the city’s future. An investment group led by Mr. Penson bought Grand Central for about $80 million in 2006. The terminal itself had little value, the lawsuit on Monday contended, because the building was under a long-term lease to the Metropolitan Transportation Authority for a relatively modest rent that declines over time.

Mr. Penson was betting, however, that the 1.2 million square feet of air rights connected to the terminal, which he bought for less than $60 a square foot, could generate hundreds of millions of dollars in a real estate boom.

The lawsuit contended that the air rights were worth $880 per square foot, a not-unheard-of sum for luxury residential projects, but one that most commercial developers believed was prohibitive for an office building.