Fast answer
The Menaggio, Bellagio, and Varenna choice should start with movement, not reputation. Menaggio is useful when western-shore range, calmer evenings, road access, Villa Carlotta, or Cadenabbia matter. Bellagio can be the stronger classic Lake Como stay when atmosphere beats logistics. Varenna is often the cleaner answer when Milan rail arrival is the fixed point. The best choice depends on ferry timing, luggage, weather, arrival route, and how many crossings the trip can absorb.
If you only do one thing
Choose Menaggio when the trip wants a practical western-shore base and does not need direct rail. Choose Bellagio for classic atmosphere, and choose Varenna when rail arrival or train returns are the strongest constraint.