The tenants association and owners of the Yorkshire Towers at East 86th Street say the proposal will make the building's midblock entrance one of the most dangerous places in the city.
According to the Daily News, the lawsuit claims the agency flouted its own guidelines and environmental review by proceeding with the plan.
The lawsuit seeks to force the MTA to conduct an analysis of the proposed single-entrance plan to the 86th Street stop.
A federal judge dismissed a similar suit brought by the same group in 2011 because the statute of limitations had passed.
The MTA declined to comment.