What is the best way to get from Menaggio/Lake Como to Malpensa airport?
I think there might be a bus that goes directly from one of the Lake Como towns to Malpensa, but we did it a little differently.
Menaggio is across the lake from Varenna. Take the ferry to Varenna. Catch the train in Varenna back to Milan. From the main train station in Milan (Centrale) take the Malpensa Shuttle (every 20 minutes; 6E) to the airport.
The one catch is that you'll need to buy the Varenna-Milan train ticket before you get to Milan as there is not actually an office to buy tickets at the Varenna station.