What fascinated me about the art museums I went to is that the building themselves were wonderful pieces of architecture and worth seeing on their own - not the case with most US museums.
Yes, the Louvre is huge and touristy but it's also worth it just to walk through the former palace.
The Musee D'Orsay was once a train station and is really a quite remarkable renovation.
The Musee de L'Orangerie has the Monet water lilies in a separate white oval room. Really stunning.
And no one's mentioned the Pompidou Center yet with the National Museum of Modern Art. It won't be to everyone's liking but it's a building with all the interior guts - like heating pipes, and escalators - on the outside. I've never seen anything like it. Plus there are street performers on the plaza outside.
http://www.centrepompidou.fr/en. Great view of Paris from the top in hallways completely encased in clear plastic.
Have fun!