New York and NJ has a reciprocal agreement. You will need to file a NY Non-resident return and NJ state return. Prepare the NY return first as that is not you residential state. When the NJ return is prepared, you will receive credit for taxes paid in NY.
Box 16 and 17 will not match for the different states.
Box 6 yes it can be deducted from NJ income
Enter the W-2s on the Federal return and if entered correctly the information will flow to each state as required.
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