This sounds like a tough situation. But one thing to consider is whether he was doing this to lighten the mood OR to put you down. I don’t think it would be good to take it to HR right off the bat. I would ask him if you could speak with him privately, and then tell him that it didn’t make you feel good when he made a comment about your stuttering. And then ask him if rather he can encourage you to speak when you are having a difficult time. Taking it to HR might just make things a bit awkward or hostile between you and the manager. I would first tell him how it made you feel, then take it to HR if he makes a comment again. I think you will come off more powerful and assertive if you do it this way. It might even help your relationship with your manager.