Beautiful seaside towns where tourists don't tread The Local
Maddogswif, and Maddog spent a short while in Santa Margherita Ligure when we traveled south from Bellagio in 1994. We had encountered a very European event, the tourist strike, where the ferry boats were on strike, but only for one day, and only for the mid day time period, thus not inconveniencing the commuters. Our train was on the East shore of Lago di Como, we were in Bellagio, the ferry was not running. Maddogswif was unamused! But Maddog's luck held, and a man whom I helped read the posted sign at the ferry terminal offered us a ride from Bellagio to Santa Margherita Ligure, a trip, if I remember correctly took about 4-5 hours. This was a real life saver for us since we were trapped in Bellagio without a hotel room, and no way to get to the train until late in the afternoon. We made SML by mid afternoon, and spent some time in the town.
SML is every bit as beautiful as Portofino, but less touristy. It sits about an hour or so north of the Cinque Terra. With the Cinque Terra limiting tourists staying in the towns, I would choose SML a base, and then travel into the Cinque Terra to hike the trail between the towns. This is the best part of the Cinque Terra anyway.
Many years ago, I arranged for friends to say in La Spezia, instead of SML. We found an acceptable hotel near the train, and they traveled up to the Cinque Terra each day. I think they also spent a day or so in La Spezia. They enjoyed the trip. Either option would be good.