If you go to the NSCA website, they provide you with schools that have strength and conditioning programs for graduate studies. I am currently in the same position you are in; gearing up for grad school. One thing you can also do is go for a graduate assistantship with a strength and conditioning program, and then go for a masters in a related area. Hope that helps.
Try and get a graduate assistantship with a strength and conditioning program. Like Mike said above you can get your master's in a related area whether its exercise science, kinesiology, etc. I would look for a G.A. position where you can learn from the strength & conditioning staff, but also be able to have some hands-on work. To me having that available and on top of going to class its a win-win situation.