All income earned while working in NJ will be taxed by NY and NJ.
As NY resident, all your income from all sources will be taxes on your NY return. NJ will tax the income earned while you were working in NJ. You can claim a credit on your NY return for the portion of the tax that applies to income sourced to and taxed by NJ while you were a New York State resident.
Instructions for Form IT-112-R
You need to prepare NY resident return and NJ non-resident return. For accurate calculation prepare your non-resident return first.
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