As rjs noted, it appears that you are a NJ resident and the period spent in PA was a temporary absence from your resident state for medical reasons. It also appears that you should have been filing in the past a NY non-resident return and a NJ resident return with a credit for taxes paid to NY.
Since PA and NJ have a reciprocal agreement, wages earned in PA by a NJ resident are not taxable by PA. If any PA income taxes were withheld, you would file a PA return requesting a full refund (easy to file a paper PA return). You would continue to file the NY non-resident and NJ resident returns.
https://www.state.nj.us/treasury/taxation/njit25.shtml
https://revenue-pa.custhelp.com/app/answers/detail/a_id/853/kw/nj%20reciprocity
