Wisconsin has a very good collegiate program, almost every state school there has some sort of watersports team, most with wakeboard teams. College wakeboarding is so early in it's development that I would say there are no good teams, only some that have good riders at one point or another. What I mean is that there is not tradition of good or bad teams, only what is currently there. I would say choose a school you like and help build the team yourself.
The University of Illinois also has a good program that was based on water skiing, but now has a wakeboard team as well.