Kyoto - No idea, nightlife there is pretty soft compared to the bigger cities. I know there are some late night areas, but probably not what you're looking for.
Tokyo on the other hand -- You can easily get yourself lost all night in Roppongi and there are bars all over Shinjuku and Shibuya as well including Golden Gai in Shinjuku (not clubs though, just small intimate bars).
You will probably be most compatible with Roppongi for the night life at those hours.