San Gimignano

I wouldn't do it by tour bus but would drive on my own. It's less than an hour away depending on where in Siena you're staying. I think either tour would work. I assume you're going during the summer? If so the crowds in both cities can be heavy but not as heavy as you'll find in Rome and other major cities.

Donna

You have to state the month of the year when you ask about Tuscany. It's also necessary to state whether you have a car. Siena is much bigger than San G, but even more crowded than San G. San G certainly has a certain amount of charm, but there are many smaller hill towns that are less crowded. Do you want to see the specific art in San G? I'll mention that in our (limited) experience, the more famous the winery, the less charming the visit. We made appointments on our own, with a car.

Let me put that another way: I don't dispute that Siena is a must-see. But you'll enjoy that San G is slightly less of a madhouse.

I don't mean to recommend a specific destination for someone I don't know, but I wanted to see the town art museum in Cortona. Cortona turned out to have 70% of the charm of San G, with only modest tourist crowds. We really enjoyed nearby Castiglione del Lago on a hot day, but you could also consider Arezzo. We loved the Aviognesi winery, but all this is quite far east, not really next to Siena.

You have 2 days in Siena. That is about right just to do justice to Siena. San Gimignano is worth seeing for sure. You could also see Monteriggioni, Certaldo, and/or Volterra on a long day.

We will be staying in Siena in September of this year. We will not have a car, we are taking trains between the cities/towns we are staying in while in Italy. This is why we are planning on using a tour to see the outlying towns around Siena and possibly some wineries....

There is a bus that takes you from Siena to San Gimignano (#130).
San Gimignano is the most visited small town in Tuscany. Obviously it must be worth it. I'd rather visit San Gimignano than Montalcino, but that is just my opinion. Both are nice, but San Gimignano is the quintessential medieval village.