I understand Wander's point, but should you decide to go via Como, travelling to Como San Giovanni station will mean that you are a long way from the boat and will have to get a taxi or take a longish walk to catch your boat. An alternative from there is the bus.
It's really not complicated to buy a ticket from Malpensa to Como Nord Lago via Saronno. The fare is around €8.75 so it is cheaper than going the long way round too. However, the timings aren't great and going by public transport almost always involves some waiting around. They just don't seem to have worked out an integrated timetable that works for tourists. Here are your three main options
A. You could aim to get the 11.43 Malpensa express from the airport to Saronno, but you might not connect with the 12.04, and have to wait for the 13.04 to Como. This would still get you to Como in time for the 14.20 fast boat that will get you to Bellagio for 15.02.
B Go to Milano Centrale by bus or train. In the middle of the day the trains leave Milano Centrale for Varenna every two hours. You are unlikely to catch the 12.20 so you would have to get the 14.20, which will get you to Varenna at about 15.30 and then you would have to get the ferry at 15.50 (car ferry as foot passengers) or 16.21.
C. Buy through tickets at the airport to Como S Giovanni Take the Malpensa Express and get off at Porta Garibaldi. Take the 13.09 to Como (no worries if you miss this one - they are every half hour and take 59 minutes). Then take the bus from outside the station to Bellagio. It goes from the station at 14.20 (you buy the tickets at the station bar) and arrives in Bellagio at 15.30.
I estimate that any of these options would cost you in the region of €20 each.
Hope that helps!
Edited: 5:44 pm, August 13, 2013