The Railway Museum is the new museum of JR East which opened at Omiya, Saitama prefecture, in 2007.
The Tokyo Transportation Museum used to be the first stop on any railway visit to Japan, but it closed and the railway exhibits were moved to the new out of centre museum.
From Omiya station catch the Saitama Shintoshi Kotsu New Shuttle to the first stop Tetsudo Hakubutsukan station where the museum is located. Walk along the under-line passage to the museum entrance.
The following locomotives are on display:
No 1, 7101 Benkei, 1292 Zenko, 9856, C51-5, C57-135, DD13-1, ED17-1, ED40-10, EF55-1, EF58-89, EF66-11, ED75-775
Plus various railcars, wagons and carriages (including shinkansen).
In addition there are drive-yourself and mini-trains, exhibits, a shop and cafe.
Current mainline stock demonstration line.
Observation deck of shinkansen, shuttle and main lines.
South building opened in 2018, with "job stations" (such as ticketing, control, engineering), simulators and history displays.
Open 10:00-18:00. Closed Tuesdays and new year. Entry fee (2018) 1300 yen.
Wikipedia web page
Museum Website (Japanese)
There was a report in Japanese Railway Society magazine Bullet-In 64.