I am 17 and I live in Fl with my mom and iwant to move in with my dad who lives in Ny. My mom doesn't agree on letting me go and said she only do it by court order. The thing is my parents are still "legally" married. So am I abje to choose?

No, you can't "chose" until you are of legal age. Even if your Dad petitions the Court for an Order you will probably be legal age before it's heard, granted, implemented.

Is there any type of Court order concerning your custody? Why are you with your mother? Their agreement at some time?