Tuscany has two airports that connect the region with the entire world:
The main connections are from Siena, Florence, Certaldo. Check routes and schedules on the website of Autolinee Toscane.
It is possible to reach the city by intermodal train + bus connection.
Line from the north: Milan-Bologna-Florence or Genoa-Pisa-Florence.
From Florence take the Florence-Siena line where you get off at Poggibonsi/San Gimignano station. Then by bus to San Gimignano.
DA Sud line: Rome-Florence.
After the camio in Chiusi/Chianciano Terme, continue to Siena. Then by bus to San Gimignano.
For all information on schedules and ticket purchases, the Trenitalia website