Como's more of a big city than a village. Are you perhaps thinking of Bellagio versus Varenna, the usual question? If so, I like Varenna the better - much prettier imo. You can get ferries around the mid lake region from either to visit the lovely gardens and other places of interest.

Como is a city with some 160 thousand inhabitants (agglomeration), 40 min by train from Milan.
IMO it wouldn't make much sense to go to sleep there if you are staying in a hotel at Milan.

In 2017, we spent three nights in Varenna, perfect thanks in part to stunning weather. Here is the part of our trip report that covers Lake Como to give you an idea of what we could do from there. Trip Report: Part 1 Northern Italian Lakes & Cities (12 days October)

What time of year? In high season, I wouldn't describe Bellagio as "quiet" until the last ferry of the night departs. I don't think I'd ever describe Como as quiet.

What do you want to see/do on the lake? Como is only convenient for sights in the town and other sights closer to the southern end of that leg of the lake. Also, Lugano.

You might want to look at the ferry timetables to understand where you can go and how long it takes to get around. The website is currently showing the winter schedules, so you'll have to check back in a month or so for the summer timetables.

Navigazione Laghi | Lago Maggiore | Lago di Garda | Lago di Como

I stayed in Como and did the lake because I like larger cities and Como is a neat old town with markets and a more real atmosphere than the tourist-oriented small villages like Bellagio - one of the biggest tourists torrents I've ever seen during day - each time a ferry comes in and ejaculated hundreds of day trippers the small town is swamped - all day -nice at night of course. Varenna which I only passed - seemed a more ordinary town with superb views. Como seemed to have few views of the lake, being set off the shoreline a km or so. I went to Menaggio and it seemed really really nice too.

We visited the old section of Como on a day trip from Bellagio and enjoyed it. However, the scenery mid-lake is much more dramatic. We prefer staying in Bellagio at the top of the town.

Very frequent service. For specific times, consult trenitalia site https://www.trenitalia.com/tcom-en

What time do you want to be at Malpensa? If using public transportation, you should allow at least 2.5 hours.

If you stay in Bellagio, another option is to ferry to Como, walk a short distance to the Nord train station, and take the train to Saronno where you can connect with the Malpensa Express train. This takes about the same amount of time as ferrying to Varenna, taking the train from Varenna to Centrale and catching the Malpensa Express train. Saronno is a stop on the Malpensa Express line, about halfway between Milano Centrale and Malpensa Airport. One advantage to this option is that the Saronno station is small and simple compared to Milano Centrale.

When checking the train timetables, you have to use Italian spellings: Varenna-Esino, Como Nord Lago, Malpensa Aeroporto T1 or T2. You can search from Varenna-Esino or Como Nord Lago to Malpensa, and Trenitalia will show you the connection at either Milano Centrale or Saronno. No need to search the connections yourself.

And there's always the option of taking a taxi or shuttle service directly to the airport. I'm not a morning person, so if I wanted to be at Malpensa by 10:00a (for, say, a 1:00p flight) I wouldn't use public trans. Here's a shuttle that picks up in Bellagio:

Fly to Lake

Malpensa airport is half an hour by bus from Arona/Lake Maggiore.
But I know that all people in this forum who have a flight from MXP want ot stay on Lake Como instead of Lake Maggiore.

There are 2 train itineraries from Como city to MXP:
Direct trains: Como SG dp 5.11, 7.06, 9.06, 11.06, 13.06, 15.06, 17.06, 19.06, 21.06 (journey time 1 1/2 hrs)
Trains with change at Saronno: Como Lago dp 5.06, 5.46, 6.16, 6.35, 6.46, 7.16, 7.35, 7.46, 8.16, 8.35, 9.16, 9.46, 10.16, 11.16, 12.16, 12.46 and then every 30 min until 21.16, 22.16 (journey time about 1 1/2 hrs)
If you com from Colico - Bellano - Varenna, travel via Milano C: Varenna dp 5.23, 6.23, 6.37, 7.37, 8.37, 10.37, 12.37, 13.37, 14.37, 16.37, 17.37, 18.37, 20.37, 21.37 (journey time 2 1/4 hrs).

Bellagio is perfect for 2 nights-no real comparison.

What time of year? It makes a differrence if it will be a weekend, too.

I'd stay in Como and take a ferry to see Bellagio. Avoid Bellagio on weekends, for sure. Maybe Moltrasio or Lario?