If I understand correctly, his choices are USAFA, USMA and civilian college with NROTC scholarship. He needs to ask himself what matters most -- being a commissioned officer, a commissioned officer in the Navy, a commissioned officer in the Navy who drives subs. The common denominator among his current choices is commissioned officer.
He should ask himself where he'd be happier if he doesn't get his first choice. Unfortunately, things can happen, whether in or out of his control. He should also ask himself where he could see himself veering should he change his mind about subs. Cadets/mids change their MOS preferences as much as civilian students change their majors.
Finally, I don't understand what you mean about Plan B or C schools not being a good place to strengthen his case. The informed advice here on SAF is that reapplicants should take a plebe-like schedule (calculus, chemistry, English, all at minimum freshman levels) and excel. Also be an ROTC stud and make a leadership impact. None of that is unavailable at a school deemed lesser than Michigan. I don't believe USNA admissions considers perceived prestige when assessing reapplicants.
Bottom line: Figure out the primary goal. Then pursue the option that gets him there. And a bird in the hand...