no actual experience, but on my list of trips to do - put in on Lewis Lake, and go up Lewis River into Shoshone Lake - a smaller lake than Yellowstone, but still pretty big,  with paddle in or hike in only access, located in the geyser basin, so lots to see.  There is one point where you have to get out and walk your boat up the river current, but apparently its easy enough to do.

Its a "standard" trip for Yellowstone - backcountry permits used to be free, and may still be, so its a lot cheaper camping.

On Yellowstone Lake, there are some areas that are non-motorized in the south end - I'd like to go back into there again someday - I hiked around the lake 24 miles to get there the one time I was there and fished the lake from shore.  Caught 20 cutthroats, all about 16" in about 1 to 2 hours fishing from my campsite (there was a slot limit, and all were within that range and released).  Shallow sandy beach area that wasn't very deep - essetially caught a cutthroat on every cast when I didn't pick up seaweed - that killed the lure actiion of the medium gold spoon I was using - got weeds 2 out of 3 times, so I caught a fish 1 in 3 casts. It was too easy.  Lakers weren't an issue back then - they were illegally introduced into the lake and last I heard it was catch and kill all you can.  

Personally, having seen fresh Griz tracks on the hiking trail, and hearing about  a woman hiker getting killed by a Griz a week or two after I hiked out, my choice would be to camp on one of the island sites.  Yellowstone is a really big lake, and wind drives some big waves on it - you can get caught, or get windbound.

You can find some trip reports over on Paddling.Net if you want more first hand accounts