You can prepare your NY return and NJ return in TurboTax. You can also make the necessary income allocations. Which version of TurboTax are you using?
When you are preparing your return, start with the Federal section and when you enter your personal information, make sure that you indicate that you have earned money in other states, in your case that would be NY.
When you get to the state section prepare your non-resident state first. You will have to indicate what portion of your income came from a NY source. Your resident state, NJ, will give you a credit for having paid tax to NY on the money that NJ will want to tax. That is why you need to complete your non-resident state before completing your resident state return.
@hgshah
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