Kinokunia in Shinjuku is great. They have 2 stores there.
You can also try Maruzen. There is one in Marunouchi, near Tokyo Station, and one in Nihonbashi. They also have many more stores scattered around Tokyo.
Kinokuniya in Shinjuku has quite big shelf dedicated for English books, you may find one there:
You can get a lot of free paper guidebook written in English at Tourism Information Center.
The truth is, whichever you got, it probably has not been updated in several years and there is better and more updated info for free online.
Take the tourist guidebooks with a huge dose of salt. Do not solely rely on them. The truth is that many have not been updated in several years. Most of them are written by “experts” who know very little about Japan, and only mention the most famous places. Rarely to never are the Japanese themselves brought in, and they know their own country better than anyone. The most accurate and up to date info is online. Many “experts” don’t have a clue that so many more great unlisted places even exist.
If you really want something to hold and read, get the official tourist guide to Tokyo. You can get it at any tourist info office and some popular tourist places - FOR FREE.
It's loaded with 80 pages of places to see and things to do in Tokyo.