If you haven't already, price out the Paris Museum Pass to see if it's worth the price. When I'm planning which museums we are likely to visit, the price has never been worth it to us. (But probably partly due to the fact that we tend to spend a LONG time in museums, so don't hit, for example, 3 museums in one day.)
Remember that your kids will be free. And that regardless, you will still have to stand in the security line. Most museums (certainly the well-known ones), you can buy tickets in advance, so you wouldn't have to stand in the ticket lines at the museum(s). This is what we have done on our last several trips to Paris. As I recall, you then have to pick them up at certain places; we have picked them up at a store near our hotel called FNAC. It looks like now, however, you may be able to buy tickets through ticketmaster - check the websites of the applicable museum.