Based on some troubleshooting tips on the New York Department of Taxation and Finance website, It does appear that New York will allow direct deposit for a return that was filed by mail.
If TurboTax will not accept the direct deposit information and the default is to receive a check, then you can hand write the routing number and account number on the state forms (line 83 of Form IT 201) when you are signing them. Just be extra careful to write the numbers precisely and legibly because the forms are probably scanned into the system.
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