Easter (and most spring and summer holidays) brings crazy crowding to Lake Como. The week before and after Easter will also be extremely busy.
The regional trains to/from Lake Como/Varenna and Milan are commuter trains, no reserved seats, and probably standing room only. Then the crowds from the trains walk down the hill, and stand in the very long lines to buy ferry tickets. We witnessed lines that were over an hour long. This is followed by lines to get on the next ferry. You cannot buy ferry tickets the day before or online.
Repeat this once you're in Bellagio. You will probably have a RT ticket, but the lines for the return ferries could be over an hour, from mid-afternoon on.
Sorry for the bad news. We experienced the above for the May 1 holiday, this past spring 2025, and Easter will be the same. This beautiful area has been ruined by the influencers.
Your only option is to go really early, get to Varenna and buy the all-day ferry tickets as soon as the ticket booth opens, around 7:30am. Then ride the ferry to Bellagio. Explore the area, and return to Varenna around 1:00pm. This still doesn't guarantee that the regional trains back to Milan aren't SRO. In addition, the regional train schedules are somewhat of a suggestion, in our very real and recent experience. Good luck!