She may file a NY resident return (IT-201), in which you have the option to file either a joint or a separate NY return. Click on this NY website for more information: Filing status - Department of Taxation and Finance. Note this excerpt:
One spouse is a New York State resident and the other is a nonresident or part-year resident. In this case you must either:
- file separate New York State returns using filing status 3 (married filing separately); or
- file jointly, as if you both were New York State residents, using filing status 2. (married filing joint)
If you file a joint New York return, NY will use all of your income to determine how much they would tax you as a couple on all of your income, and then prorate the amount to the percentage of your overall income earned by your spouse. Separate returns will calculate her tax amount on her separate return. You would not have to file a NY return since you have no taxable NY income.
If you do choose to use the Married Filing Separately status on your state returns, here is how you may do so: https://ttlc.intuit.com/replies/3301995
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