If anyone's still wanting to know...
Ebisu has a decent game center right near the station (forget which exit) called Aso-Viba. Their IIDX/GFDM machines are crazy loud. The keys are good and only 100en.
Shibuya has a few.. one was closed for renovations and bought out by Namco, I believe, but should be open soon, if not already. Before they closed it, DistorteD was 100en and there were three machines. Popolare has two IIDX at 200en, but the arcade is pretty snazzy and the keys are great.
There are so many in Tokyo, no need to name the specific locations. If there is somewhere in particular you wanna go (like in and around Yamanote line), just ask
