I guess it depends on what you want. I prefer sightseeing to beach and don't mind doing some driving.
Venice has more to see and the water taxis would be fun for children. It is always busy in my experience. I last went in May a couple of years ago (without the kids) and it was full of American tourists. But Venice is an amazing place to visit. Unless you stay on the Lido, you won't get a pool.
Personally I don't like the Lido but that's just me however it would be a good place to stay with children because you do ge the access to the beaches.
Pisa is smaller and less to see in my opinion. Plus beware if you want to go up the Leaning Tower, under 8's aren't allowed to climb it. When we went last my 2 were both under age and we had to leave them with my BIL who doesn't like heights!
There is a beach resort close to Pisa but it's pretty typical Italian ie private beaches with loads of sunbeds next to each other.
I would recommend San Gimignano, Tuscany and the countryside around there. Have been several times. I love San Gimignano, which is a beautiful walled town. Last time we went my 2 were 4 and a half and 2 and we hired a villa with a pool and mixed it between sightseeing and swimming. The kids loved SG and the narrow streets and towers and ice cream! We also flew into/out of Pisa so managed to do that as sightseeing and we got the train to Florence from Certaldo train station, which is also a good place to stay. There are lots of little, beautiful apartment complexes with shared pools around there. But you'd need a car.
ps Can you tell I don't like Italian beaches????