There are a number of lesser known museums in Paris. Those places are great especially because there are fewer tourists so you're not going to be stuck waiting in long lines and you can take your time once inside.
I second the Marmottan (Monet) museum in the 16th. The collection is really impressive, especially the basement.
The Jacquemart-Andre Museum in the 8th is also great, as much for the furnishings and art as for the house itself. The cafe is also a really nice place for tea or dessert in the afternoon, and the nearby Parc Monceau is beautiful.
Have you done the Saint-Chapelle on the Ile de la Cite? I think it's easily the most beautiful tourist site in Paris with incredible stained glass. If you do go, you may want to check ahead as they've been cleaning the windows and you might not be able to see everything.
If you're looking to be outside more, there are some beautiful lesser known gardens such as the Bagatelle in the Bois de Boulogne.
You could also check out the covered galleries (pre-cursor to the modern department store) that run from the 1st above Palais Royale into the 9th. They get progressively seedier (and cheaper) as you go north, with some pretty cafes, chocolatiers, antique shops, and booksellers. That's a great activity especially if it's a rainy day.