We are flying in to Malepensa, and are staying in Bellagio for the first 3 nights. Which is quicker, cheaper, (or more convenient): Milan to Varenna and boat to Bellagio, or Milan to Como and boat to Bellagio?
The Malpensa train takes you right to Como, where you can catch either a boat or a bus to Bellagio.
I'd take the bus from Malpensa to the Milan Central Train Station. Then train to Varenna as you suggested and take the ferry to Bellagio. Once you arrive in Varenna, it will be about a 10 minute walk from the train station to the ferry dock but it's mostly downhill.
I loved Rick's suggestion of getting picnic supplies at Gilardoni Alimentari in Bellagio...they make great sandwiches and have slices of a memorable apple tart!
Enjoy Lake Como!
If you go to Como to p/u ferry make sure to check schedules and it is a slow ferry.
I have taken ferry from Varenna to Como in AM and it is infreq and slow.
We spent a week in Bellagio a few years ago, and we rented a car to get there. We also enjoyed having the car to explore the area. Most days, we didn't use the car. But, when we did, we were thrilled to have it.