There is no train to San Gimignano. The medieval towers sit on a hilltop with zero rail connections. You have three options: bus (cheap, easy), car (fast, flexible), or guided tour (zero thinking). All work.
Step 1: SITA bus or train from Florence to Poggibonsi (50 min by bus, 30 min by train, €4.50). Step 2: Bus 130 from Poggibonsi to San Gimignano (25 min, €2.30). Buy a Tiemme ticket at the tabacchi in Poggibonsi.
Firenze–Siena superstrada (free), exit Poggibonsi Nord. Use P2 or P3 parking outside Porta San Giovanni — €6/3h. Don't drive into the center — ZTL.
Most tours combine San Gimignano + Siena + Chianti wine. GetYourGuide and Viator list dozens.
Bus if budget-conscious. Car for flexibility (combine with Volterra or Chianti). Tour if you want everything handled.