Idaho is full of great places to play on and in the water so making a 'best of' list is really hard and definitely open to argument! Some people like to travel up into the mountains or go away from civilization before they put in to water-ski. You'll probably notice that most of the choices I made below are easily accessed and close to home. So check out the list and then argue away!
Murtaugh is a lake that most people either love or hate. It isn't very deep and it often has a lot of moss. Because of that it usually isn't crowded and still allows for some long straight runs. It is also easy to access and has great camp and RV sites...boating is free but camping has a charge.
Salmon Dam is one of my favorites on this list. We go out there usually at least once a year. Similar to Murtaugh the water usually has a lot of green in it but the reservoir is so long that you can really just ride for miles if you want. Plus there are some nice sandy beaches that you can float your boat up to and set up for a day camp. You can put in at the docks or at Greys Landing. Perk - you can camp and boat for free!
Lake Walcott is one of the nicer places to ski. The water is always nice and the camp sites are great. Other activities include disc golf, fishing, hiking, and cabins for rent.
Thousand springs is one of the best places to water ski. The stretch of river is long and straight. The water is usually really cold though so it is nice that the hot springs are so numerous in the area!
This is another one of my favorites because it is close to home and there is just something amazing about skiing between the towering walls of the Snake River Canyon!