Between the two, I'd go with San Gimignano. It's slightly bigger, with more options for eating. Parking is just outside the city walls from what I've seen, but we've never driven a car in Italy. Cortona has a newer lower town, and of course the hilltop village..there is also parking outside the walls, but your hotel in either town could have some parking available.
From San G, it's an easy trip over to Volterra - which has some wonderful Roman ruins and Etruscan museum. (we rode our tandem from San G to V, so you can certainly drive it!)
We really enjoyed our second visit to San G, there is a tower you can climb and a fun fortenzza to explore, plus the piazza is a great place to sit and enjoy your gelato.
San G will be noisier and busier during the day, but after the buses leave to go back to Florence, the town is abandoned and fun to explore...
Honestly, you can't go wrong with either one...if you've never been, don't worry about which is better..but since you have a car, you can visit both in any case.