Per the New York Tax return preparer e-file mandate web page:
If you can't e-file the return because it's not supported by your approved e-file software or it can't be filed on our Web site, then you aren't required to e-file it.
Additional information for preparers is available on the New York State website:
Penalties for both Preparers and Individuals are outlined on the New York Electronic filing mandate for business taxpayers website:
If you or your preparer are required to file a tax document electronically and instead file on paper, you're subject to the following penalties:
In addition, any overpayment claimed on a return that was required to be e-filed won't be eligible to receive interest until the document is filed electronically.
Note that any link in the information above is updated each year automatically and will take you to the most recent version of the document at the time it is accessed.