we have been to basel for a weekend so didn't see much, but we went to the Tinguely museum and our kids (2 and 4) loved it. It's at the end of a beautiful park and to get there we had to take the ferry acrtoss the river- great fun as well.
A boat ride sounds good fun too, and i think you can swim (although not sure it's safe for little ones).
I've heard the zoo is great, too.
We really liked Basel, seemed like there was plenty to do, and we are planning to go back (we live in Geneva now)