You will file a New York resident return and a New Jersey non-resident return. You should complete the nonresident New Jersey return first, followed by the New York resident return. It is important to complete your taxes in that order. New York will issue you a credit for tax paid to another state (New Jersey). Completing the returns in that order will ensure the calculations are correct.
Your New Jersey return should only have your New Jersey income on the nonresident return. Your New York return will also include your New Jersey income. As a New York resident, all of your income is taxable by New York, regardless of where it was earned. As you go through the New Jersey return, you will be able to allocate income taxable to New Jersey.
If you and your spouse were nonresidents for the entire tax year, and your are the only one that has income from New Jersey sources, you can file a New Jersey nonresident return using the Married/Civil Union Filing Separately status. Your wife may also use that status, even if you filed a joint federal return. You also have the option of filing a joint nonresident return, but you will have to combine your income and deductions.
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