They have a great science museum. Older ones might like the creepy (very!) catacombs.
Definitely go for one of the big art museums - Orsay's top floor is full of very famous impressionist paintings. I find the Louvre a bit overwhelming, but they could see Mona Lisa if they wanted to. Or the modern Pompidou Centre which has amazing street performers outside.
If it's open, a climb up the towers of Notre Dame is great as you can get right up close to the gargoyles.
Definitely the Eiffel tower. The Bateaux Mouches boat rides are pretty especially at night. Shoppers will love Champs Elysees.
Take them up to Montmartre to the artists' square to have their caricatures done? Great cafes up there and usually lots of street performers.
I don't know if this thread is still active, but I saw you weren't going to Paris until May. We decided to create our own food "tasting tours" that involve things like finding your favourite desserts (macaroons, crepes, ice cream, etc.). We also did a boat tour at night (like the above post suggested). If you want to do something for free then just walk around by the Seine at night so that you and your kids can see the gorgeous monuments lighted. My kids had a lot of fun doing a scavenger hunt with this scavenger hunt book, 'Mission Paris' (we bought before leaving) We also enjoyed going up to the top of Montparnasse Tower - incredible view of the city- without the wait of the Eiffel Tower.