I am not clear on the implications or advisability of filing both a joint New York nonresident return at a joint New Jersey resident return. You may want to have a professional review. In any case, your wife’s HSA contributions will be excluded from her taxable income on her federal return and they will be added back to her income on the New Jersey return.
If any of her HSA contributions through payroll deduction can be allocated to the period of time when she was working in New York, they will already be excluded from her wages. You can’t take an additional deduction. If she made separate additional contributions from out-of-pocket funds which are separately deductible on the federal tax return, they would be allocated to New York if the contributions were made during the time she was working in New York.
