Best location/town to stay on Lake Como

Middle lake is the best and with train access from Milan points you to Varenna. To go to Lugano, you can cross the lake on the ferry to Menaggio and get a bus to Lugano from there.

Another vote for varenna

Varenna, Bellagio, Menaggio, Cadenabbia, are the 4 mid-lake towns with the most frequent boat service, since they are served by the mid-lake shuttle ferries.

I like all the above towns, although there isn't much in Cadenabbia.

Varenna is popular because it is served by the railway. If you plan to have a car, and plan to see Lugano, then Menaggio is probably the best option, since there is plenty of free parking (both street and at few lots), and you need to go to Menaggio anyhow to go to Lugano. If you don't have a car it doesn't really matter which town you stay, because even if Bellagio and Menaggio are not served by the train, they are just minutes away from Varenna by ferry.

But Argegno does not have direct rail access from Milan, or any rail access for that matter. Train to Como and then either a bus or lake boat to Argegno. To visit Lugano, back track to Como on the bus (because it stops at S. Giovanni station) and get a train to Lugano.

It is true that Argegno has less frequent boat service, and no train service, but Argegno has a helipad, so it's convenient if one uses a helicopter.

The easiest town to travel to Lugano, Switzerland is Menaggio. You add a ferry ride to a bus ride if on the other side of the lake.

But train access is on other side of lake. So can’t have both.