In Epcot, between Mexico and Test Track, I think it used to be the odyssey restaurant (pardon if I spelled it wrong). They are never crowded and always clean.
In MK I like the restrooms near the Baby Care Center/first aid off Main Street, they are always clean and always a CM in sight in out outside of them.
my favorite restroom has to be the one at Rafiki's Planet Watch. It has bright colors, animal sounds and the bathroom stall doors have facts about....poop