Are you living together? Who is the child with now? If you're not living together and you have the child then you just need to take control of your life and leave him out of it?Don't call him, don't go see him, do not invite the drama into your life. Do not ask him or his mom for help of any kind, and let your life be YOUR business. You may be trapping yourself by being too dependant on them.
Are you married or were you? If so, you will have to deal with the legal aspects of custody. If not, he will have to prove that he is the father even if he's named on the birth certificate. Most states favor the mother in these cases, given that you are a fit parent, not abusive to the child, can support him, and are not on drugs or involved in anything illegal. Running away will only get you into trouble. Kidnapping is a federal offense and it gets worse if you cross state lines.
Is the father abusive to you or your son? Verbally or mentally? Physically? Abuse of any kind is tough. We condition ourselves to believe what we are being told about ourselves. We tell ourselves that we deserved the names we're called or that we asked for the bruise on the arm. Though it's terrifying you have to get out. Call the police, let them take him in and get out during the 24 hours that he's gone.
Honestly, if you're waiting for the right moment to leave, you're never going to find it, you just need to step up and do it.