Just mail it. There is an exception in NY that you don't have to e-file if the software doesn't allow it. (In this specific case, the requirement that a state return can't be e-filed unless the federal is e-filed first or at the same time is a security procedure put in place to help the states prevent fraud. A few years ago there was a rash of fraudulent state returns where crooks would file several state returns claiming large fraudulent refunds, without filing matching federal returns, because the states had much weaker fraud detection methods.)
