Yes. Income earned in NY is taxable in NY no matter the source. NJ will also tax this income but will give a credit for the income tax you pay to NY on these same earnings. For your self-employment income, you can determine the amount of NY income by dividing the amount of gross pay that you earned in New York by the total amount of gross pay reported on the 1099, and then multiplying this percentage by the amount of net income reported at the end of the Schedule C. (You may use that same percentage against reported deductions, such as 1/2 of self-employment tax deduction or the self-employed health insurance premium deduction) This is what is calculated for your NY nonresident return,
If you are not sure how much gross income you received in New York, you may need to do further calculations. If you have paid receipts or invoices use these. If not, you will have to figure out your NY portion by dividing NY work days by total work days, and then using this percentage against gross income. Then you can proceed as above.
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