If you can afford it, I think Northeastern should certainly be in the running. I can’t say know the physics department here well, but I think you are very right to compare by department and not just the school as a whole.
I would say that UR, Amherst and RPI would all be players along with Stony Brook. I myself applied to UR and almost to RPI. Neither was insufficient academically, the co-op program and the feel of the school (a true good sized campus in the middle of Boston with plenty of access) made me apply/choose accordingly.
It sounds like you have plenty of great options. I think at this point your son should start to focus on his personal preferences knowing that all current options are affordable (yes?) and academically comparable. Best of luck!