It all depends on how long you intend to stay and whether you'll have a car.
If you don't intend to drive, then Pisa, Lucca and Florence have easy rail connections between them. Siena's train station is quite inconvenient, so I've tended to use the coach. My recommendation would be to stay in the centre of Florence and make day trips to the other cities... or not! There's so much to see in Florence that you could easily spend a fortnight there without being bored. Well, I could anyway.
(As an economy tip: Tuscany's spa towns are overprovided with hotel accommodation, so you can often get real bargains. Montecatini Terme is on the rail line between Florence and Lucca, and is pleasant enough as a base.)
If you intend to have a car, you might consider taking some rural accommodation. It's what I've tended to do in recent years -- you can take a break between fighting the tourists in Florence and spend a day relaxing by the pool instead.
