Don’t be afraid to go to the Musee du Louvre with kids. I think it could be interesting, even for them: there is a medieval castle in the basement, king apartments furnished, crown jewelery, Egyptian sarcophagus… Most kids will love to see “real mummies” in the Egyptian section, and go downstairs to the Medieval Louvre, where they can see the old walls exposed. Napoleons apartments are neat also, chandlers the size of small cars, how the rich and or royal lived.
The Musee Rodin is the very best because you can just go for the statuary in the gardens and there are some great sand boxes in the back, as well as a fairly decent cafe.
Another great one to go with kids is the Cinema museum at Bercy. Lots of tourists miss this one, but it is interactive and cinema is a very important part of French culture.
If you are looking for an art fix that is also fun for kids, I highly recommend the Pompidou Modern Art Museum.
Musée de la Poupée it`s for girls, boys and theirs parents. It`s very artistic.
The Arts et Metiers – particularly the chapel with the history of powered transport and the Foucault pendulum, also the Theater of the automates (you often need to book this in advance) and the “bat plane” over the stairwell
Musee Galleria has a great fashion exhibit right now about Castelbajac that kids seem to love. It is so much fun and creative
The National Museum of Natural History in the Jardin des Plantes and there is a nice little menagerie/zoo there for kids too. If you enter the Jardin des Plantes from the northwest corner off rue Linne in the 5th and walk towards the Seine and when you exit cross the main road (there are crossings so find them first) there is also a nice open air sculpture museum beside the Seine that the children would probably enjoy as you walk back to the Ile St Louis and a Berthillon ice cream.