I'm not sure if I should let my son stay the weekend with my mom and slightly creepy step father?

NO, YOU ARE NOT overreacting. It is your job to protect your son. Your gut is telling you something is wrong. Just because you don't have proof doesn't mean nothing is wrong. Find a way for your son to spend time with your mom without being alone with your step dad and keep your eyes open to changes in behavior. I have seen way to many kids hurt by just this type of situation. Please do not let it happen to your son.