Hi Courtney!
Well, first let me tell you what I did. I got my Masters in Nutrition but did my concentration in wellness rather than the clinical nutrition. This way I got some core nutrition classes but then my concentration allowed me to basically take exercise physiology classes which I really enjoyed and I feel are essential for working with athletes.
I guess your first question is what do you want to do? Do you know that you want to work in sports nutrition?
If so here are your options to think about:
masters in sports nutrition (this may be too specific if there are other things you are interested in)
master in exercise physiology ( if you don't choose this option just make sure you do take some classes. Sports RDs need to have knowledge of at least the basics of ex. phys.)
Master program that combines some ex phys and nutrition
I am sure others that took a different route will have even more advice to share :)