Heritage Museums and Gardens, Sandwich. The Cape's biggest cultural site, and the strongest single wet-day option: changing galleries, an American automobile collection in a round barn, a working antique carousel, and a hundred acres outside for when it clears. Allow half a day.
Sandwich Glass Museum. The Boston and Sandwich Glass Company made this the Cape's one genuine industrial town through much of the nineteenth century. The cases are fine; the reason to go is the live glassblowing, which holds an audience of any age.
JFK Hyannis Museum. Photographs and film rather than objects, covering the Kennedy family's summers in Hyannis Port. The compound itself is private and not visible from any road, so this is the whole of what can be seen.
Cape Cod Museum of Natural History, Brewster. Small, thoughtful, and perfectly sited on the marsh. If the rain eases, its own trail runs from the back door out toward the bay flats.
Whydah Pirate Museum, West Yarmouth. Built around a real wreck: a slave ship turned pirate flagship lost off Wellfleet in a storm in 1717 and found in the 1980s. Conservation work on recovered material is visible on site, which is the interesting part.
Provincetown Art Association and Museum. The Cape's serious art institution, holding work from an artistic community that has been here since 1898.
Woods Hole. A small federal aquarium with local species and rescued seals, alongside ocean science exhibits from the research institution next door. A very good hour on the Upper Cape.
The National Seashore visitor centres, Salt Pond in Eastham and Province Lands in Provincetown, are free, warm, indoors, and have films and exhibits worth an hour. They are the cheapest wet-day answer on the Outer Cape.