Hello youcandoit76:
Thank you for your kind words, and for your follow-up questions.
You should be able to file a Form 1040 federal tax return as a permanent resident (a.k.a. a Green Card holder), and then file a NY nonresident tax return (or a resident tax return if you would prefer), all without jeopardizing your federal immigration status. In fact, whatever you end up doing with New York state won't affect your federal status in any way -- as they are two completely separate things. And no, I don't think that you're being unduly paranoid at all. In fact, I can absolutely appreciate your caution and thoughtfulness on this issue.
With respect to the TurboTax program: yes, you're probably going to run into that issue regarding a program recommendation on which NY state return to file. As explained in my original answer, while the TurboTax guidelines may be correct for 99%+ of all users, it is not necessarily "right" in every single case . . . especially when it comes to unusual issues like this regarding residency. That said, if you qualify for the (federal) Foreign Earned Income Exclusion (Form 2555 on your federal return) by virtue of living overseas, then it really won't matter which NY state tax return you file, because NY will honor the federal income exclusion anyway.
Thanks again.
