Akihabara seems to be much more place to enjoy during the day but there are some interesting night spots.
Such as train themed Izakaya "Little TGV". At Little TGV, you sit on a real used train seats, and eat train themed decorated dishes, drink train themed cocktails, and be served by waitress with train themed costumes. This is an example of Akihabara-like (otaku-like?) place you can go at night.