I only have 2 nights to spend in Lake Como area (early september) and will be departing Lake Como for a 2 night stay in Cinque Terre. In terms of booking accommodations Are there any other towns (other than Varenna that seems to be booking up quickly) that would be easy to get to and from via public transportation? I will be coming via train from Venice.
All of them are easily reachable by public transportation. There are ferries that connect all of them. From Varenna you can take ferries across to Bellagio, Menaggio and everywhere else. Along the Lecco to Varenna rail line there is also Mandello which is nice. It comes not long before Varenna, on the Lecco branch of the lake.