Having recently visited the Australian Maritime Museum, I would have to say that is one of my favourites. There is so much to explore and it is very interactive, making it ideal for children. Going up to the top of the lighthouse and visiting one of the tall ships was a highlight, closely followed by the "Rescue" exhibition for kids.
I recently visited the Australian Museum for the first time for Jurassic Lounge and was very impressed with the size of the place and amount there was to see. I didn't get to have a good look at the permanent displays because I was preoccupied with the temporary events on the night but I definitely want to go back. It's seems to be everything you want in a museum and covers so much, from dinosaurs to insects to Australian animals.