A child born out of wedlock then parents marry and seperate what rights does the father have?

In a normal custody agreement parents usually need the permission of the other parent to take a minor child out of state. Unless you're doing something to endanger your child's welfare, not a court in this country would let the father take your child away from you, and there's something very wrong with a dad who would suggest it. However. if dad will be in NY, file two petitions - one for child support (even if he's paying it's always good to have it in writing in a court order), and another for an order of protection preventing him from not only taking the child out of state but from coming anywhere near you and your son. If your son's dad wants visitation rights, let him file a petition - and the visitation must take place in New York, and since he's threatened to take your son, I would demand that  it to be supervised.