Hi. I was there in May.
You are spending several hours on the boat if you use that route to Como. What would you do with that time instead? Would it be more interesting/worthwhile than the boat ride?
Also, how far is it from the boat dock to the train station in Como? It's only a short walk in Varenna.
We stayed in Varenna, and took the train both in and out. Because there were some issue with the place we were staying in Milan (they only took cash, and it actually was difficult finding an ATM to dispense it, as they apparently have serious issues with ATM theft in Milan), I was glad we did so. But if I had had plenty of time, we would have taken the boat, just like you are thinking of doing.
As long as you are going in a season other than winter, I wouldn't worry at all about calm water.