Although NY does have an e-file mandate, you cannot e-file a NY return independently of the Federal return. This is universal to all states, even in states where there is no mandate. NY does have a way for you to input the information onto electronic forms on their website Enhanced Form IT-203, Nonresident and Part-Year Resident Income Tax Return.
However, if this option is not viable, you still may mail-in your NY return. They may likely send you a letter, but you will be able to explain that you were unable to e-file the NY return because you mailed in your Federal Return. There is no longer a penalty for not e-filing a NY return.
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