3 nights in Santa Margherita Ligure

What kinds of things do you enjoy? There is a large park that abuts SML, Portofino, and Camogli, Portofino Regional Park. It has all levels of trails and is much less crowded than Cinque Terre (which includes Riomaggiore). The ferry and bus allow you to do any combo of those three places and enjoy the park. Portofino is tiny and so I'd try to head over to Camogli as well.
If weather does not cooperate, I'd check out Rapallo or Genoa.
https://www.apathtolunch.com/2014/07/portofino-ferry-boat-schedules-from.html

Be prepared for lots of crowds in Riom and the other Cinque Terre towns.

Crowds can be a problem. However, for me, the highlight of the Cinque Terre was seeing them from the sea. Take the ferry along the coast to see them. It stops at all the villages on the coast itself so you get both a close up as well as a further distant view of the area. I've done it twice.

There may even be a ferry from SML to the Cinque Terre.

As for Portofino, unless you are a shopper, you won't need a whole day to see it.

Unfortunately, it appears the ferries to CT from SML stop in September, but the local ferries should still be running (see the Path to Lunch website for links to the ferry schedules).

We spent 5 nights in Santa Margherita Ligure in late June (2024) . The crowds may not be as much of an issue in October (or they may be.) It was particularly crowded in Portofino. What worked well for us was we got the earliest ferry we could to Portofino, immediately walked up to Castello Brown and had it mostly to ourselves before the crowds starting coming in. Castello Brown is well worth it with spectacular views looking down on Portofino. We had a snack and coffee at the cafe up at the castle before walking back down to the harbor. By the time we got back to the harbor it was quite crowded and we were ready to get on the ferry out of there. But we were so glad we went. Portofino is so lovely. Definitely recommend going as early as you can. We loved Camogli. It was one of our favorite day trips. It's only a 5 min train ride from SML in the opposite direction as the Cinque Terre. You could go to Portofino in the morning and to Camogli in the afternoon. To get to the Cinque Terre, we took the earliest train we could to Vernazza. It was not crowded in Vernazza at all in the morning and we had a nice breakfast by the harbor. Then we took the ferry from Vernazza past the Cinque Terre villages (with the exception of Monterosso, which comes before Vernazza) and saw them all from the sea, and it was spectacular. The ferry was also surprisingly uncrowded. Maybe we just got lucky. We took the ferry all the way to Portovenere, which is not actually a Cinque Terre village but just beyond the 5 villages and is full of charm. It's also a good village to visit to get away from the crowds. We had the best pesto of our lives at a little shop called Bajeico la Bottega del Pesto that sells take away cups of pesto pasta. After spending several hours in Porto Venere we took the ferry back to Riomaggiore and from there took the train back to SML. One tip for SML, try to eat dinner at Ristorante Oca Bianca. Get reservations. This was the best meal we had in SML. Sooo good.

Walk to Rapallo and take the bus back. The walk is pleasant with quite a few points of interest: historic mansions, a monumental cemetary & WWI memorial, beaches, an historic church with a Van Dyke painting, and Rapallo itself has much of interest including a chairlift up to the Sanctuary of Montallegro with stunning views of the Portofino peninsula: https://www.apathtolunch.com/2018/10/a-beautiful-seaside-walk-along.html
Note: The ferry schedules on apathtolunch.com have not been updated since the pandemic.