Como has two railway stations, both linked to Milan, so a day out in Milan is feasible if you are really organised and are not staying too far up the lake to get the last bus back from the station in the evening. The mainline station is San Giovanni, situated on the western edge of the city, about a ten minute walk from the lake area. From here you can get to central Milan (Centrale) in as little as 45 minutes. The Como Nord Lago station is right on the lake front, so very convenient, except that trains to Milan (arriving at Cadorna) are stopping trains and quite slow as far as Saronno.
There is no railway line up the west coast of the lake. The main line coming up from Milan Central veers away from the lake after Como, going on to the border at Chiasso, for connections into Switzerland. But down the eastern shore there are frequent trains connecting all the main towns and villages to Lecco and Milan. From Lecco there are also connections to Bergamo.
For exploring the Lecco leg of Lake Como, and further on up the Eastern shore, the train is probably the best bet. Every sizeable centre on this shore has its own station, and the line provides a good route to Milan if you fancy a day out in the city. Direct trains run from Varenna to Milan Centrale every two hours and take just over an hour. The last train back leaves Milan at 21.20, and the return fare is just over €12. You can get a return ticket that includes metro and bus travel for just €16 for the day*. Before you get on the train you must validate your ticket in the machine at the station. Failure to do so may land you a hefty fine, and pleading ignorance is no defense, unfortunately.
The northernmost station is at Colico. So if you are staying on the northern stretches of the lake, it’s pretty feasible to take the bus, or drive, up to Colico and jump on a train there for a trip to Lecco or Milan. Train travel is cheap and generally reliable.