Syntrax Nectar has a "Naturals" line which uses stevia instead of artificial flavorings. I've got the peach, and it's okay, but for me it does have a weird aftertaste. I believe they did have several flavors of it available, though.
There are quite a few unflavored whey protein isolate powders available, and you can use flavoring extracts along with the stevia to make shakes with that. Not too bad, I've done some with that. I like
All The Whey | Whey Protein Supplements for Bodybuilding and Health also, they're just starting to make some with natural sweeteners instead of artificial, but they've got good plain powder to mix as you want.
Good luck with your search more and more of the protein powder manufacturers seem to be coming out with naturally sweetened ones.