Definitely Pisa and Lucca. I've done it before, and it's quite easy. From Santa Maria Novella station in Florence, the train to Pisa takes about an hour and fifteen minutes. If you're most interested in the Leaning Tower and the other sites around the Piazza dei Miracoli, be sure to get off at Pisa San Rossore station, NOT Pisa Centrale. That will save you a long walk.
From Pisa, there are two trains per hour from San Rossore station to Lucca and the ride is only 20 minutes. From Lucca back to Florence it's either an hour and twenty minutes or an hour and forty five minutes, depending on which train you board. The ones that leave at 0:31 past the hour are faster.
Personally, I would recommend going to Pisa first, then Lucca. You could judge your time better that way, and perhaps even stay for dinner in Lucca. It's a charming town, very walkable, especially if you take the path that runs along top of the city walls. And if you still have strength in your legs by afternoon, consider climbing the Torre Guinigi. The views are spectacular!
I would recommend a full day in San Gimignano, mainly because the bus takes quite a while (with a connection in Poggibonsi), and you ABSOLUTELY need a full day in Siena.
I hope this helps.