We want to daytrip to Portofino and Cinque Terre. Right now we have a hotel reserved in Santa Margherita, but that's 50 miles from the CT. What is the smartest way to see both places? We have 3 days there.
Easy! Train.
(I'm really a novice at this) Is Santa Margherita a good home base then?
You're in a very nice area. Depending on when you are going, the CT can be a zoo. It's about a 1hr. 20min train ride to Riomaggiore, the farthest of the 5 towns from Santa Margherita Ligure-Portofino. One thing you will miss out on is the special 3-day pass sold by Trenitalia for the CT. The pass is good for unlimited rides on all trains between Levenato and La Spezia. It's also good on the trails between the towns (yep, they have ticket booths) and it's good for the vans in each town that climbs the steep hills and, it's good for the open air museum that's there somewhere. I suppose it the pass is of use to you, you can buy roundtrip tickets from Santa Margherita to Levanto and use the pass for the remainder.