Fast answer
For most first Lake Como base decisions, choose Varenna when train arrival, easy ferry access, and a compact old-town stay matter most. Choose Bellagio when the larger visitor center, restaurants, and central-lake pull matter more than rail practicality. Bring Menaggio into the decision when western-shore routing, Cadenabbia, villa days, or a less Varenna-Bellagio-focused trip shapes the plan. None of the three is a universal winner: ferry timetables, train returns, tickets, luggage, weather, restaurants, events, and onward movement decide the right base.
If you only do one thing
Use Varenna as the default when the trip starts or ends by Milan train and you want a smaller base with ferry access. Move to Bellagio only when the trip is built around its visitor infrastructure, and consider Menaggio when western-shore movement is not just a side trip.