According to the NY form 203 intructions here, you must file a joint NY state return if you file a joint federal return. You will only be taxed by NY on the NY source income. It is usually better overall to file jointly (FED and state) than separately.
In the NY state interview you will allocate to NY only your NY income. NY will use a ratio of your NY source income to your total income. That ratio is applied to the NY state tax as if both of you are resident to arrive at the tax on NY source income. TurboTax will make those calculations on the forms automatically based on your allocation inputs.
If you wish you can prepare returns both ways, joint and separate, to figure out which yields the better overall tax result. This is easiest using a TurboTax desktop product where you can prepare several returns.
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