I hven't taken the girls to the museum, but exDH did, again only a few weeks ago.
The first time he took DD2 she was 2 and loved it.

May I suggest a third option, though? Both my girls have always *adored* SciTech and Scinece Works and have gone from a young age - so I would suggest Science Works as a great and interactive place that will keep them both amused.