If you worked in NY, you have to pay NY taxes – its a privilege of working in NY. You must file a NY non-resident tax return. You must file as married filing jointly and include your wife’s name and SSN but can omit her income on the NY tax return. There is another form you fill out w2here you basically verify that your wife had no NY income. You must also pay NJ taxes because you lived in NJ. On the NJ joint tax return, you will get a credit for your NJ state taxes for the taxes you paid in NY.

If you only worked in NY for half the year, you only include that amount on the NY tax return.