Generally transport museums seem to be photographer friendly, on several occasions I've taken loads of photos at the National Railway Museum in York and the London Transport Museum Depot in Acton (some of both are on Commons, the rest will appear at some point when I've got around to sorting them. Don't hold your breath).
The Museum In The Docklands (near Canary Wharf) were also fine with photography iirc, but there wasn't much there that would photograph that well.
Chris