Touring Tuscany for 3 days

We stayed outside of San Gimignano on an agriturismo. You can find bed and breakfasts at Booking.com and other web sites. Virtually every farm in the region has rooms and/or apartments as a source of secondary income.
Be sure to rent a car so you can get around to the different hilltowns. We loved visitingCertaldo, Siena, San Gimgiano and Volterra--and just rambling throughout the countryside.

You'll be visiting in the Harvest in October. The region is even more interesting at that time of the year.

If you are without a car I would say Lucca for 1 night and Siena for 2 nights. From Siena make an excursion to San Gimignano, and to Pisa from Lucca, if time allows.

We're taking a train from Venice to Florence where we would rent a car. Is Siena close to Florence?

David, I see your a fellow southerner. I live near New Orleans. When did you visit Tuscany?

Siena is about an hour away from Firenze - look at rome2rio.com for time estimates for different modes of travel.

1hr22min from Florence to Siena by train. Perhaps better to rent your car in Siena to avoid Florence traffic. Where do you head after Tuscany?

We thoroughly enjoyed Volterra.

After Tuscany we head to the amalfi coast by train. I so appreciate all of your input!

Perhaps continue on from Siena to Orvieto via Montepulciano. Return your car there and get a train to Rome, then onwards to Naples.

Siena to Orvieto via Montepulciano

We did this and had a wonderful time. Just wished we would have spent more time in all three places and then some.