The big museums in New York are all uptown, and Lower Manhattan gets written off as a place you pass through on the way to something else. That's a mistake. What we have down here are small museums, the kind you can walk into for an hour and actually finish, and most of them sit within a 20-minute walk of each other.
We get asked for nearby things to see a lot, usually by guests with half a rainy afternoon and no plan. This is the list we give. It's short on purpose. Every place below is one we can point to on a map from our front door on John Street, and the hours and addresses come from each museum's own site (they do change, so check before you walk over).
One practical note before you go: nearly all of these are closed at least two days a week, and they're not the same two days. The Skyscraper Museum runs Wednesday to Saturday, the Seaport Museum runs Friday to Sunday, and the 9/11 Museum is closed Tuesdays. If you've only got one afternoon, check the day first and build around what's actually open.
How to pair them up
Two museums in an afternoon is the right number, three if you're quick and it's raining. The easy pairing is the Seaport Museum and the 9/11 Memorial & Museum, since they sit on opposite ends of the same walk and you can cut straight across on Fulton Street. The other pairing is Federal Hall and Fraunces Tavern, both old-New York, both a few minutes apart down by Wall and Pearl. Battery Park City and the Skyscraper Museum are a separate trip, best combined with a walk along the harbor rather than with another gallery.
If you're staying with us, you've got a kitchen in the suite, which changes the math on this kind of day. Go out for the museum, come back and make lunch, go out again. You don't have to plan the whole day around restaurant hours.