I recently visited the Mariners’ Museum in Newport News, Virginia. Wonderful museum near Williamsburg that is worth a visit if you are in the area. Any other examples?
The Watermen’s Museum in Yorktown and the Virginia Living Museum in Newport News are other favorites of ours, although we haven’t been in years.
Nice thread idea!
Not sure how “hidden” these are but since they aren’t super huge:
Peabody Essex in Salem, MA https://www.pem.org/
Currier in Manchester, NH http://currier.org/
Colby College Museum of Art https://www.colby.edu/museum/
walking tours of Philly’s murals https://www.muralarts.org/tours/
Ringling in Sarasota, FL https://www.ringling.org/
El Museo del Barrio in NYC http://www.elmuseo.org/
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In Chicago - this one is a very different museum - International Museum of Surgical Science - https://imss.org/
@sirpher1 There is also the Mutter Museum in Philadelphia , a medical museum. Also, in Philadelphia is the Mummers Museum, which is interesting. Also, the American Swedish Historical Museum- my grandmother was Swedish so I particularly enjoyed it, although it is a little off the beaten track.
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The Museum of the City of New York is a gem chronicling the history of NYC.
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The Federal Reserve Bank of Atlanta has an Atlanta Monetary Museum that is fascinating. You get to see counterfeit money there, and robots that carry stacks of bills around and shred them up. When I was there, they were handing out bags of shredded bills to all visitors to keep as a souvenir.
https://www.frbatlanta.org/about/tours/museum.cfm
Some of our recent favorites:
Mutter Museum, Philadelphia, medical history and medical oddities
Norton Simon, Pasadena, a really impressive art collection for a small city museum
Museum of Flight, Seattle, cause I’m nerdy that way
Also in Philly: Eastern State Penitentiary
https://www.easternstate.org/
Although I haven’t been at that time of year, their special events at Halloween are supposedly great if you are into that kind of thing.
@doschicos We drove by the penitentiary and it certainly looks interesting. There was a long line and we did not have advance tickets but would like to take a tour if we get back to Philadelphia. We have also driven by the West Virginia State Penitentiary, in Moundsville, which also is very old and gives tours and has spooky events!
The Hyde Museum in Glens Falls, NY http://hydecollection.org
The Norman Rockwell Museum in Stockbridge, MA https://www.nrm.org
The Clark Museum in Williamstown, MA http://www.clarkart.edu/mobile/home
Mass MOCA in N. Adams, MA http://massmoca.org
Briscoe Museum of Western Art San Antonio (on the Riverwalk) http://www.briscoemuseum.org
In the last few months we have also visited the LBJ Presidential Library in Austin and the JFK Library in Boston. Both a very worthwhile visit.
Colby has a remarkable museum for a school that size. Bowdoin’s art museum is also excellent. I’ve seen a number of really outstanding special exhibitions there, in particular.
Also not “hidden,” but not as well known as places like Williamsburg and Sturbridge Village is Strawbery Banke (yes, that is the way it is spelled, and they aren’t trying to be cutesy 
) in Portsmouth, NH. Just a fascinating place.
Strawberry Banke, Portsmouth, NH http://www.strawberybanke.org/
Whaling Museum, New Bedford, MA https://www.whalingmuseum.org/
Literal gem museum - the Lizzadro Museum of Lapidary Art in Elmhurst IL. http://lizzadromuseum.org/ It has a great little gift shop for interesting pieces (especially jewelry) at various price ranges.
MacArthur Memorial (museum) in Norfolk, Virginia. Douglas MacArthur.
Woodrow Wilson Presidential Library and Museum in Staunton, Virginia.
And in Pennsylvania:
Johnstown Flood Museum - fascinating and heartbreaking.
Jimmy Stewart Museum in Indiana, Pa.
Andy Warhol Museum in Pittsburgh.
A big second to the Peabody Essex museum in Salem, MA. It’s one of our favorites.
Also, here in the Phoenix area, the Musical Instruments Museum:
So many of my favorites already mentioned (Peabody, Museum of flight, rockwell). But I did think of a few more
Barnes Foundation in Philly
Museum of History & Industry in Seattle
Wing Luke Museum in Seattle
The Morgan Library & Museum in NYC
Frick Collection in NYC
The Phillips Collection in DC
National Postal Museum in DC
Princeton University Art Museum in NJ
The Corning Museum of Glass NY state
I’ll second the Musical Instrument Museum in Phoenix and the Museum of Flight in Seattle.
All three of my kids loved the Arizona Museum of Natural History in Mesa, AZ. It’s not huge but it’s well done. We visited many times and they never tired of it, even when they were well into their teens.
On my list to go to in the Boston area are the World War II Museum in Natick, MA https://museumofworldwarii.org/ and the Museum of Russian Icons in Clinton, MA http://www.museumofrussianicons.org/
Two of our family’s favorites:
In Amsterdam- http://www.torturemuseum.com
In Rome - http://www.theculturemap.com/bone-cemetery-visit-capuchin-crypt-rome/