The service you want is more important than the school for that service.
That said,
USAFA: slightly tougher academics (based on the ONLY people to make 4.0 some semesters were at USNA on exchange), a little more individually oriented (based on feedback from exchange mids), focus on pilots (1/2 the classes currently go to UPT).
USNA: (less experience here) Many more choices for careers. The Marines have a little of everything, and the Navy is a bit more diversified in its missions than the AF.
AF: Air, Space, and Cyberspace
USN: Subsurface, Surface, and Littoral warfare.
USMC: Littoral warfare from the sea (mostly ground and air)