If you decide on Cooke City we usually go up the Goose Lake Jeep Trail. It's groomed(oftly rough sometimes), but will take you to Lulu Pass. If you climb over that and go north from there it will drop you down in the north side of Henderson Mountain. Great riding back in there. Just watch for avy's there! Lots of playground.
Togwotee? We used to stay @ the lodge. Mega expensive! I think their cabins are in the 250-275/night range which sleep 3 comfortably. Now we just stay down in Dubois. Lots of night life, good food, small crowds. It's a 30 minute drive to the top to ride, but not a big deal. Roads are usually well maintained.
Snowies? Fun mountain range. Been hitting this playground hard for the last 15 years. Lots of rocks before January. The best snow in the Snowies doesn't hit until late January/early February. Offers more diversity in riding styles. Hillclimbing, pow playing, trail riding.
My money would be #1 Tog(if with the ladies), #2 Cooke, #3 Snowies. Hope this helps