The lake has one city and a string of villages, and the choice is really between an evening that exists and a morning view that does.
Como — the city end
A working city at the southern tip with the cheapest beds on the lake, two stations, bars around Piazza San Fedele and forty minutes to Milano Centrale. The trade-off is that the famous villas and the best water are an hour north by boat.
Varenna — the quiet eastern shore
Small, steep and directly on the Milan–Sondrio line, with the car ferry across to Bellagio and Menaggio from the same waterfront. It has perhaps a dozen places to sleep and they sell out months ahead in May, June and September.
Bellagio — the postcard, at postcard prices
Staying here buys you the village after the day boats leave, which is the only time it is calm. Parking is minimal and expensive, the lanes are stepped, and room rates are the highest on the lake.
Menaggio and Tremezzina — the practical western base
The western shore has supermarkets, a lakeside lido, buses along the SS340 and ferries to everywhere, plus Villa Carlotta and Villa del Balbianello within a short hop. Pick one base on the central lake and let the boats do the moving; splitting nights between the two arms wastes a day.