Getting from Milan Malpensa Airport to Varenna?

Malpensa Express train from Malpensa to Milano Centrale.
Then Regional train from Milano Centrale to Varenna.
If you need to go to Bellagio, from Varenna there is a ferry that crosses the lake to Bellagio.
Varenna is obviously easier to reach than Bellagio, because it's on the same shore as the railway.
Bellagio can also be reached by bus from both Como and Lecco, at the southern tips of the respective lake branches.
However the roads are tortuous and buses are not as frequent as trains.
Another alternative is the boat from Como to Bellagio, scenic but takes a bit longer.
Varenna and Bellagio are in the midlake, which is the most beautiful part of the lake and both are very quaint.

Como is a larger city, not a village. Lecco, at the southern tip of the other branch is also a larger town. Neither one would is my cup of tea, although I've made the mistake to stay in both in the long gone past. I'd stay in Varenna or Bellagio.

Trains timetables

AIRPORT TO MILANO CENTRALE
http://www.malpensaexpress.it/en/
(make sure you take the right train to Milano Centrale, not Milano Cadorna, which is a different station)

MILANO CENTRALE TO VARENNA
http://www.trenord.it/EN/

You can buy the tickets all the way to Varenna at the airport station.
Remember to validate (date stamp) your ticket at the machines before boarding the train.

Hi Carol,
We did this trip last year and it was easy to negotiate from the airport to the train station and out to the lake.
The previous response gives you the detail.
We stayed in Varenna which was lovely and we traveled by boat to Bellagio. I think either town would be delightful.

Enjoy your trip

I actually like the city of Como, but Varenna is a nice little town with easy transportation links.

Thank you for your advice & for the links to the train schedules! (I was confused by the variety of trains in Italy.) Much appreciation--Carol

Carol,

It's actually a very easy trip from Malpensa to Varenna, although it can sometimes seem a bit grueling after a long flight.

The trip from Milan to Varenna takes 1H:03M. DON'T forget to validate your ticket prior to boarding the train on the day of travel, or you'll risk hefty fines which will be collected on the spot! I'd suggest sitting on the left of the train (when facing forward) as that will provide the best views of the lake. Be prepared to disembark promptly in Varenna, as the train doesn't stop for long.

We were in Lake Como in the fall of 2014 and stayed in Varenna because it is more convenient for train travel. We took ferry to Bellagio & other villages and villas. Varenna is lovely!