This relationship should be entirely up to your son as it's only his step-father. Have you asked your son how he feels? Even very small children (as soon as they can speak) will be quite blunt as to whether they are comfortable with one or the other of the parents. It sounds to me your son is not accepting his step-father so I'd start paying closer attention. It's not like you are taking him away from his biological father. I have seen where very young boys (even 3 - 5) can be extremely protective of their mother and this appears to be the case in your situation. It's highly possible he would just like a peaceful life with just the two of you and the step-father is right out of the picture. I am not sure if your ex had adopted your son then you will need to see a lawyer, but if he didn't then you can see a lawyer and take total custody of your son. Often a judge will talk to the child in his/her chambers and it's all about what is best for the child. It's also possible that the step-father may just relinquish any custody he has with your son.
I would like to add that perhaps your son should not have a strong relationship with his stepfather who is narcissistic. That could lead to bad modeling for your son and possibly deliquency. Also, narcissists traditionally lack empathy, so do you really want to teach your son to have a relationship with someone who doesn't care about him? A question back to you is how do you know the stepfather is a narcissist? Psychologically speaking, a narcissist would never admit to it because they don't believe something is wrong with them. If you have had to speak to a counselor or psychologist and got this diagnosis for him, then you already have problems and to subject your son to that any further would be more damaging. My advice to you: RUN. Just go in the opposite direction and don't look back. I was in your son's position before, and now they have split up, and I don't talk to my stepfather or my mother. So she was hurt twice as bad. While your narcissistic husband may not have empathy, you do. So please use it for your son and don't try to force him into a relationship with a man like that.