If you choose to file a joint return with your wife, all of your income gets to be taxed by New York.
No matter what state you live in, your state of residence gets to tax all of your income. It doesn't matter where it was made when you are a resident. However, you get a credit on your home state's return for taxes paid to the state(s) that you earn the money in. The credit is featured rather prominently in the New York interview, as its a commonly used one.
You are not required to file a joint return with the State of NY if one of you is a resident and the other is a nonresident. You can choose to do so, but if you do, you are agreeing to be taxed as a NY resident.
See NY return instructions, page 13:
https://www.tax.ny.gov/pdf/current_forms/it/it201i.pdf
If one spouse is a New York State resident and the other is a nonresident or part-year resident. In this case, you must either: (a) file separate New York returns using filing status 3 or (b) file jointly, as if you both were New York State residents, using filing status 2.
