What career are you aiming for? School choice makes a big difference if you want to coach vs do research vs work in cardiac rehab. Each school has its speciality area, biomechanics, ex phys, nutrition, etc.
A few of the top exercise science programs are:
UMass, Penn State, UDelaware, Wake Forest, UNC-Greensboro, UConn, Arizona State, Illinois, Maryland, Indiana U., Oregon State, Texas A&M, Wisc, Michigan, Michigan State.
Most of these schools were ranked because of their PhD programs, but I think it's safe to assume the Masters programs are decent as well.
Depending on the program, it might be difficult to use eligibility. Your advisor may decide that since the dept is paying your way, you need to spend your time working for them, not running.
I just noticed you said you want to work with runner and endurance athletes. Not to burst your bubble, but chances of that happening are very small. The need (read $$$) is not with athletes, but with general health, the aging population, and the obesity epidemic. Even for that type of research, the government is not handing out as much funding as they were a few years ago.
If you want to work with athletes, get your coaching certification from USATF. Combine that with your experience, and you should have a better chance of landing a job and working your way up the coaching ladder.