Yes, you need to file in all three states.
Your wife's income is taxable on her CA resident return.
Your income earned while working in NY is taxable on your New York non-resident return.
As a resident, New Jersey requires that you report all of your income, including what you earned in New York. However, they'll give you a credit for your New York taxes so you don't get double-taxed.
Just make sure you prepare your New York nonresident return first, so we can apply the correct tax credit once you get to your New Jersey return.
CA allows you to file MFS when filing jointly on your federal since you were a nonresident for the entire year and had no income from California sources during the year.
NJ allows you to file MFS when filing jointly on your federal when one spouse is a resident and the other is a nonresident of New Jersey.
For NY, Separate returns are required for some married taxpayers who file a joint federal return. If one of you was a New York State resident and the other was a nonresident or part-year resident
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