Akihabara gathers many many such stores. Such as Mandarake, Liberty, Gamers, etc. Liberty is more focused on second hand video games. Those shops are gathered along Chuo-Dori, which is pretty obvious since it is the biggest street in the area.
If you want to find generally new manga, just visit any bookstores in the town. You can find tremendous amount of new releases and some old ones too. One of the biggest bookstores in central Tokyo is Junkudo in Shibuya.
If you want to find some English version, find bookstores from this article: