I ask because I tried look for listings of places I know well (e.g. Turin, Italy or Budapest, Hungary) and found that the closest entry was hundreds of miles away.
Turin has, for example, this: http://www.museodellafrutta.it/en/ which is pretty niche, imho. Budapest has a chocolate museum: https://www.csokolade-muzeum.hu/bemutatkozunk/ and so on...
The one I would be recommending (to the niche museums site, and also to everyone who is around) is the Yokohama Coast Guard museum.
It has a really unassuming name, I only went in because I got caught out in the rain without an umbrella in Minatomirai. Dare I say it is the best museum I have ever visited. It is organised around a single curious event: In 2001 a Japanese Coast Guard vessel encountered a suspiciously behaving fishing travel. They wanted to board them when the fishing vessel took off at high speed and started shooting at them. During the pursuit they even seen the crew wield shoulder mounter missile launchers.
Turns out it was a North Korean spy ship on a mission to raise funds by smuggling drugs to Japan. The incident ended by the Korean crew scuttling their vessel. The coast guard has raised the sunk ship and built this museum around it.
Website of the museum: https://jcgmuseum.jp/en/
More info on the event: https://en.wikipedia.org/wiki/Battle_of_Amami-%C5%8Cshima
Some other personal favourites:
* Molson, Washington - it's a preserved ghost town, somewhat like Bodie, California, but one can go inside nearly all of the structures, and there is an actual museum set up in the three-story former town school.
* Not sure this counts, because The Met isn't a niche museum overall, but their Egyptian wing is the only place I've been to where one can walk through two more or less complete ancient Egyptian structures without going to Egypt.
My favorites are the Clockarium, Museum of the Art Deco Ceramic Clock. (https://www.clockarium.org/ Check out the video, its is magnificent.)
And The Sewer Museum: Experience an authentic sewer, stroll along the Senne and discover the little-known but ever so important profession of a sewage worker. Descend deep into the bowels of the city for this unique experience! https://sewermuseum.brussels/
Who didn’t want to know what happened to East London Victorian Sewage.
Or the mysterious cave of shells which no science know it came to be [I suspect due to lack of interest, lols]