Our boys adored the Musée de l’Armé (it’s big) – we went twice and only saw two wings plus napoleon’s tomb.
They also loved the Musée du Moyen Age (metro stop is Cluny Sorbonne).
I’d suggest Musée d’Orsay over the Louvre.
And the Rodin museum was great. We invested in the audio guides, and the kid’s audio guide for the ten year old, who loved it.
If you are planning lots of museums and galleries get the museum pass (check what is included) http://en.parismuseumpass.com
Check if there are visiting exhibitions — we never got to the Eiffel Tower but spent half a day in the Hergé exhibition at the Grand Palais that we only learned of from metro posters once we arrived.
Download the Next Stop Paris app, for how to get where you want from where you are via metro.
If you want grass to run around, etc, go to the Luxembourg Gardens. Nice description here (scroll down a bit): http://www.thesestolendays.com/what-to-do-and-not-to-do-with-children-in-paris/
Our other Paris tip is not walk 1.1km to get THE baguette from THE boulangerie the blog post recommended. Just go to the nearest place that doesn’t look like a tourist trap 😉
But I bet you’ve worked that out by now.