We have taken the train from Switzerland (Lugano actually) to Como (about 40 minutes by train), then stayed in Bellagio for several days. We took the slow ferry up from Como and the hydrofoil when leaving, walking to and from the train statin. When we left, we took the train from Como to Venice (connecting thru the main station in Milan). We much prefer trains as renting a car has always been problematic and stressful for us. It's definitely personal preference however as to renting a car or taking the train. If you are staying near the train station and travel light, with no mobility issues, the train works for us. We don't like to worry about parking, ZTL zones, tickets arriving after our trip or dealing with rental car companies not in our native language. We found that the trains in Switzerland (we've spent about 6 weeks total there traveling exclusively by train) to be the gold standard, meaning the trains are spotlessly clean, on time to the minute and very easy to navigate, generally relaxing and scenic. Italy trains (traveling about 3 weeks over 2 different trips) are way better than Amtrak in the US, however not as clean, not as efficient, scenic unless going into or out of a big city, as most trains in Switzerland. And yet we've almost exclusively taken in train especially in Central and Northern Italy.
Milano Centrale to Como is about 40 minutes by train or to Varenna on lake Como is about an hour. Also, both towns are reasonable times on the train to many parts of Switzerland depending upon where you are going next. I can't speak to the weather that time of year as we were on Lake Como in early September.
I would say after lots of museums, art and the big city of Milan a few days in the smaller villages and towns around Lake Como would be wonderful. Have a great trip.
