You can reach Bellagio by boat from most of the towns around Lake Como. Consider that boat trips are slower and, obviously, more expensive.
If you’re traveling from Milan to Bellagio and prefer this option, I’d suggest you to get off at Como Nord Lago and reach the pier which is located in Piazza Cavour, Como (a 5 minute walk from the train station).
The cool thing is that Bellagio is right in the middle of Lake Como, and is probably the best place to go if you want to visit more towns during your holidays.
For this reason, if you are in Bellagio and want to visit Varenna or Tremezzina, just head to the pier, buy your ticket and reach the destination you want!