Ciao Maria,
Biggest question is this: what is it you want to do and see on those 5 days? This is to determine how much you want to be able to move around the region. If you want to see museums or just roam around, taking it easy. Luckily, Easter week is end of April this year so weather should be nice so spending time outdoors should be top of the list as well.
So you have two options: if you want to see a lot in those five days, the car will make it easier to move around.
With a toddler in tow, you'll need to work around his schedule and not force him too much to adapt to yours.... but with no train schedules to worry about, it will make it easy to change plans as well as give him a chance to take naps on longer travel times.
With 3 kids myself, that is what I'd suggest to make life easier. I can tell you that even when there was just one in tow, the car was what we used to explore around Tuscany because it made it easier to cut a visit short and head back out to the car and move on to the next stop.
In this case, with a car, location doesn't matter too much. You can most definitely choose something closer to Pisa, but you can head out to Florence, Siena, explore Chianti on another day, San Gimignano. I'd suggest a place between Florence and Pisa, such as
Podere Casanova or
Agriturismo Poggiacolle, both are very family friendly. If you want to be more centrally in Chianti,
Agriturismo La Sala is also a cool place to stay at. I also like
Montalbino, because they have animals on the farm and kids love those!
Second option: take it more laid back and
not rent a car. It will limit your day trips but you will have more time to stay put and explore your location. I would suggest either Florence or Siena as your base, maybe in this case Florence wins out. It is well connected to the region so if you were to want to try a day trip, you can take a train to Arezzo or Lucca or take a bus to Siena or join a guided tour into Chianti. The guided tours provide transport so it makes it easier to explore the Chianti area without worrying about schedules on public transport.
Of course, a stroller will also be essential, as you don't want to carry your son in arms once he gets tired, and he can also take naps there. I hope you have a sturdy one that can go over cobblestones well as streets can often capture wheels and provide for a very jumpy ride, one that is not conducive to naps for the kid.
You can then spend time exploring museums and the many sights, allowing your son time off out of the stroller as well and letting him explore and roam. As for places to stay in Florence, there are many options: you can start your search by looking at the
family friendly hotels and B&Bs on Florence Accomodation and then go from there.
There will be lots of people on Easter weekend wherever you end up at, it is just a major occasion for lots of people to take time off. April 25 is also a national holiday in Italy so it is likely many will have the week off. I'd suggest making a decision soon about where you want to be located and try to book ASAP if you haven't done so already!
