If you're planning to visit Siena and will be leaving Florence to get there, try taking the bus: it's faster, easier, and costs about the same (around €6.50). Make sure you take the RAPIDA, or express which arrives in Via Tozzi, just a ten minute walk from Piazza del Campo in the heart of Siena.
Wondering which airport to choose?
Pisa and Florence both have airports, but their services vary considerably. The most (and cheapest) flights are available from Pisa for little or no difference in cost for reaching Florence's center, Santa Maria Novella Train Station: