The arcades are in the main drag or in the old part of Akiba. They all have many floors of which the ground (1st) will be UFO (crane game), There is normally a floor for medal games and a floor for card based games.
My personal haunt is in old Akiba in the same street as KFC (east/west) The upper floors have alot of space and a wide selection of games.
Taito is ok and Sega is a bit cramped.
Google Maps
And this is the shopping arcade with the 7 floors of goodies...
Google Maps