This is a tough decision. I have stayed at Park Hotel Vitznau and Beau Rivage, and both were excellent. I have not stayed at FS Geneva, but it also has an excellent reputation. Still, I would probably tend to reduce the 3 nights in Geneva to 2. If you reduce Beau Rivage to 1 night, the stay risks being quite rushed.

Also take into account the weather, though. If it rains, there is more to see and do in Geneva than in Lausanne, I feel. The activities you can do from Beau Rivage are essentially outdoor activities (such as: boat tour on Lake Geneva, visiting the vineyards of La Cote, ...).