I think all of the museums are worth the price of admission. The kids always have a great time, no matter what museum we go to, except for the art museum ..."I'm so BOREDAHHhhhh!"
I went to the Aquarium for the first time last spring and was pleasantly surprised. Its not as small as I thought it would be. I could definitely spend more time in there. Quite a few of the exhibits were very calming and just beautiful.
I grew up around the philly area and have hit all the museums, numerous times. They are definitely worth seeing. The old architecture alone is worth it to me.
We take the kids to the aquarium and the Franklin every year. The boys like the natural history musuem cuz of the Dinosaurs. The Franklin has ALOT of interactive stuff for the kids. Go EARLY to that one so that you are not rushed. The kids like to spend ALOT of time in there. With kids, you could easily spend the better part of a day in there.
If you are bringing kids, try the Bug Museum. The kids loved it! Adults, not so much, its' small and a bit disappointing for the adults I think, but We did get a good laugh listening to all the "Eww gross" comments.
The kids can hold a tarantula, and Hissing cockroaches. I did learn more than a thing or two at that place. I thought it was cool. The bug museum is a bit of a hike from the other museums, but was good to do on a rainy day.
Don't forget about the Philadelphia Zoo either. It's a really nice zoo with some really nice inside exhibits. Teh zoo is something else that we hit with the kids once a year.
Mummers Museum if you or the kids are into costumes.
At the waterfront, there is a civil war era ship you can tour, as well as a submarine that you can tour. Both are pretty interesting if history or ships/subs grab your attention. There is also maritime museum there that is also nice, has some interactive stuff for the kids. I was a member of that for several years.