TSUTAYA Shibuya has large floor dedicated for manga. It's faced to the famous Shibuya crossings so it is easy to find and access as well.
If you are looking for English translated manga, this article may help you:
- 7 Bookstores In Tokyo To Go English Manga Shopping
I would suggest the Shosen Book Tower (書泉ブックタワー) in Kanda. They're building from 1st to 9th floors are filled with books, and you can find many kinds of Manga there!