I think the main issue is that most of the folks who invade our pristine waters don't realize what affect they have on the others around them.

The best course of action is to slowly cruise up to the offending boater, introduce yourself and calmly explain that the sets you are running are difficult to do with all those boat wakes and is it possible for them to stick to another part of the lake for a short spell until you've gotten your sets in.
We had this issue a few years ago, I was pulling my boys on wakeboards and we were just killing the ski course. The guys did as I suggested above and I was more than happy to oblige (and after having had it pointed out to me felt bad that I hadn't noticed what we had done).

This was before my boys started true slalom skiing and we had an appreciation for how hard it is when the rollers start. We have the same issue now with barefooting.

Bottom line, take the low key friendly approach, it usually works.

If not, "accidentally" running over their tow rope works too......not that I would condone such un-neighborly behavior.

Chris