Transit Museums, North America
Museum of Science & Industry

The MSI is one of the premier science and technology museums in the US (if not the world). It is a huge museum located Jackson Park. The visible museum above ground is nearly as big as the underground part of the museum. They recently completed an expansion for a German U-Boat that had been displayed outside, now is underground in its own exhibit hall (I was there before it opened). 

The museum has several railroad displays, including a huge model layout depict a line from Chicago to Seattle. This is a must visit museum even for the non-rail fan.