According to the forms instructions you would include her income. But her income will not be taxed for New York State purposes. As a nonresident, you only pay tax on New York source income,
Per the forms instructions:
Married nonresidents and part-year residents, who are required to file a joint New York State return, must use the combined income of both spouses to determine the base tax subject to the income percentage allocation, even if only one spouse has New York source income. You will compute a base tax as if you were a full-year resident, then determine the percentage of your income that is subject to New York State tax and the amount of tax apportioned to New York State.
However, a spouse with no New York source income cannot be required to sign the joint return and cannot be held liable for any tax, penalty, or interest that may be due. This form will allow the Tax Department to properly process your return.
This will be used to determine your part time residence apportionment of New York State Tax.
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