Santa Margherita - boat tour to Portofino or to Cinque Terre in Sept?

You can ferry hop from Portofino to the cove/abbey at San Fruttuoso around the peninsula to Camogli - and then take the train back one stop to S.M.L. That would be fun. I spent a few days in Camogli last May (loved it!) and hiked part of it and took the ferry part way. S.M.L. is lovely too.

I have been to the Cinque Terre a few times. It's great, just very touristy, perhaps overly so. It's very easy to get down there from S.M.L by train and take a ferry between various CT towns. Really up to you. It's just going to be crowded down there, even in September, but if you don't mind that, the CT towns are lovely.

There is a local bus that goes between SML and Portofino. It takes about 20 minutes. It's what the locals use.

When I stayed in SML, I took the train to Monterroso and hopped the ferry between villages. Just be aware, if the weather isn't good, the ferries may not run.

The CT was crowded with tourists. However, walking around SML I mostly saw locals. That was in May.

From SML to Cinque Terre use the train. The tour boat had only one tour this year by reservation. It takes longer and limits the time of your visit to a few hours in 2 of the towns.

With a week I see no reason not to do both, but like the others, I see no reason to pay for a tour when there are regular ferries to Portofino, or you can take advantage of the wonderfully uncrowded trails through Portofino park.
Likewise, I would train to CT and make use of ferries.

Portofino is very close to Santa Margerita Ligure. We took a boat from the town dock one time and have driven tnere a couple of times too. Parking can be difficult even though there is a public garage. We met people who walked there as well. You will not need to spend a whole day there, a very pretty setting, designer shops, expensive restaurants, but also very small.