How big of concerts are you looking for? There are a lot of cool concert venues in Tokyo. Just in Shibuya alone, there must be 5+ decent sized venues including
Shibuya AX,
CC Lemon,
O-East,
O-West, etc.
In Harajuku, there is one of the most famous large concert venues, the
Yoyogi National Olympic Stadium - many large JPop and JRock bands play this venue each year.
Here are a couple of listings of concert venues in Tokyo:
List of Tokyo concert venues
Venues List