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There are a couple of mix-and-match ways to do this beyond the obvious car-rental, private shuttle, or car-and-driver service options, and I thought it would be nice to have them all in one place ...
WEST (COMO-COLICO) BRANCH:
TO COMO: Catch the Malpensa Express train to Saronno station run by Le Nord (leaves from lower level of Terminal 1), change for Como Lago (end of line). Tickets sold at Malpensa just above the platforms, no need to book in advance. [Times can be consulted at the TreNord web site (no English as of yet, but pretty basic interface -- use input Da: "Malpensa Aeroporto" A: "Como Lago")]
Como (Nord) Lago station is right across from the waterfront, so if you're staying in Como, you've reached your destination.
ON UP THE LAKE: From here you have two main options:
1) Cross the street to the left to the ferry ticket booth and catch a ferry or hydrofoil directly to destination town.
[Boat schedules can be found at the lake navigation web site.]
2) Catch a bus from the depot/information area across the street to the right.
[Bus schedules may be consulted at the SPT line web site.]
*NOTE* It's also possible to follow one of the options below, then
catch a ferry from Varenna over to Bellagio -- usually this is a bit
more trouble (you'll need to come a few hundred meters, mostly downhill,
from the Varenna/Esino train station to the ferry, and backtracking to
Milan Central isn't the most direct way to the central lake), but
sometimes the times work out to be similar to the train/ferry combo
EAST (LECCO-COLICO) BRANCH:
TO TOWNS LECCO-COLICO (inclusive):
You start out with two options from Malpensa to Milan -- either:
1) Catch a Malpensa Express *train* to Milano Centrale
[Times can be consulted at the TreNord web site (no English as of yet, but pretty basic interface -- input Da: "Malpensa Aeroporto" A: "Milano Centrale")]
2) Catch a Malpensa Shuttle *bus* to Milano Centrale [Timetable and online tickets available on their web site.]
TO & UP THE LAKE:
From Milan's Central Station you can then catch a regional train (usually headed for Tirano or Sondrio) to Lecco, Varenna/Esino, Bellano or Colico. For stops between Lecco and Varenna (Fiumelatte, Lierna), you'd need to get off at Lecco and change to a more local train heading in the same direction.