The Kyoto Railway Museum (https://www.kyotorailwaymuseum.jp/en/) is certainly worth a mention. Tons of well-preserved examples of Japanese rolling stock, including multiple generations of Shinkansen (including the first!). Their technical explanations of every part of the train were also incredibly well done, with lots of examples from parts of real trains. It was one of the most impressive and genuinely educational technical museums I've ever been to.

Having been to both the National Railway Museum in Taipei and the Kyoto Railway Museum and comparing the two, I'd say that the former was particularly strong in areas around train maintenence, whereas the latter had much more content about trains themselves.