I'm sure I'm missing some but here goes

Air Force Academy (Cadet Area): 7200 ft
University of Wyoming: 7165 ft
Northern Arizona: 6950 ft
Colorado School of Mines: 5675 ft
UC Boulder: 5430 ft
New Mexico: 5312 ft
Colorado State: 5000 ft
Utah: 4783 (Presidents Circle)
BYU: 4630 ft (Lavell Edwards Stadium)
Nevada: 4505 ft

There's also a number of smaller colleges in the Rockies in Western Colorado, including Colorado Mountain College, the highest US university at over 10k ft.

I expected to compile this list and point out what am advantage BYU has, but it's quite clear they're not the only ones. By my count, BYU is the 8th highest D1 university in the country, which is an advantage but not a unique or prohibitive one.

BYU has really taken it and run with their advantage in a way that Air Force, Wyoming, New Mexico, Colorado and Utah haven't