If you are married and filing a joint federal income tax return but one spouse is a New York State resident and the other is a nonresident or part-year resident, you are required to file separate New York State returns. The resident must use Form IT-201, "Resident Income Tax Return." The nonresident or part-year resident, if required to file a New York State return, must use Form IT-203. However, if you both choose to file a joint New York State return, use Form IT-201 and both spouses' income will be taxed as full-year residents of New York State.
So you can file your federal taxes as Married Filing Jointly and your NY taxes as married Filing Separate. That way you can avoid paying NTC taxes on your portion of income.