I'm not sure about any of the following, because I stayed on the lake this year rather than day-tripping from Milan
I think it might be better to take the train from Milan to Varenna and spend all your limited-in-December daylight hours in the mid-lake area. The fastest trains to Varenna (hourly at 20 minutes after the hour) take just over an hour. Now you're in one of the places you want to go and have access to the mid-lake ferries. If you instead take a train to Como, it won't take quite as long, but you'll have a fairly lengthy ferry ride to Bellagio. I like the idea of a loop trip rather than retracing my steps, too, but you'll have very limited time on the lake, and you may want to spend the maximum amount of that time in the scenic, mid-lake area.
If you're unlucky with the weather and still want to take a side trip up to the lake, I suppose going to Como--which has a few museums--might not be a bad option. I can't say for sure, because I haven't been to any of the Como museums. (An alternative destination would be Bergamo, with a very atmospheric hilltop upper town.)
If you do decide on the train to Como, check to see whether there are convenient trains to the Como Lago station. That should put you closer to the ferry dock. Going to Como Lago will add a few minutes to the train journey, but it might be worth it.
Take care when you research the train schedules on trenitalia.com. There are departures toward Varenna from at least three different Milan train stations.
