Seems like Clemson does. I know there are a lot of wakeboarders there due to their proximity to a large sparsely populated lake. I know UGA used to have a watersports club but I'm pretty sure they didn't actively compete. Not sure of their current status.
University of TN does. I just graduated from there in December of 06. Its a club team. I wasn't on it but a friend of mine's brother was on it. They had a Mastercraft X9 i think. Don't know what they have now.