We stayed in Bellagio, despite initial hesitation about it being touristy, and I'm glad we did. The waterfront can be crowded in the daytime, but unless you want to hang out there, it's not an obstacle. Just go somewhere else--up the hill, down the street, across the lake. In the evening and early morning, Bellagio is heavenly.
I reviewed the Hotel Florence in the hotel and restaurant review area--highly recommended--as well as several Bellagio restaurants.
Visit the Villa Carlotta. The gardens are lovely, the views spectacular, and the museum not overwhelming.
My main complaint about Lake Como is the ferries. They are expensive, dirty, and the schedule is beyond belief confusing. But all that could have been overcome by some pleasant staff. We visited 5 countries this summer, and never had one single bad experience with the local people. Except on the ferries on Lake Como. The ferry staff--on board and in the ticket offices--is universally irritable, unhelpful, brusque and unpleasant. And, of course, interaction with them is nearly unavoidable. Granted: dealing with tourists, docking and boredom can be a challenge, but the guys running the boats from Sestri Levanti to Portofino could give these people lessons. They liked their jobs and it showed. I have no good suggestion for avoiding this problem--the whole point of Lake Como is being on the water. Just wanted to ensure your expectations are low.