Most of the novels by Haruki Murakami are set in (at least in part) in Tokyo and he has a nonfiction work, Underground, about the gas attack on the subway system in 1995. I would recommend:
Wind-Up Bird Chronicle
Kafka on the Shore
Hard Boiled Wonderland at the End of the World.
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In the Pool by Hideo Okuda
Empire of the Signs by Roland Barthes
Legless in Ginza: Orienting Japan by Robin Gerster
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This might not be what you are looking for (Its non-fiction), but it's a really great book: Tokyo Underworld by Robert Whiting.

It tells the true story of an Italian American who came to Tokyo after WWII and built a restaurant that laid the foundations for what is the Roppongi party district of today.

But along the way it explains the interesting relationship that the governments of Japan and America have with the Yakuza (Japanese Mafia)

And it tells the story of why Pro Wrestling is so popular in Japan (I'm not a fan, but it was really interesting to learn about)

The stories it tells are crazy enough that you might think it's fiction!
Source(s):
http://www.mahalo.com/tokyo-underworld
http://www.mahalo.com/robert-whiting

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You might want to check out cell phone novels! Most of them are actually originally written in Japanese and are set in or around Tokyo. You can find them translated on Amazon. The most interesting thing about them? They are entirely written via text messaging. It's revolutionary. Check it out!
Source(s):
http://en.wikipedia.org/wiki/Cell_phone_novel

http://kotonoha.monkey-pirate.com/completed-series/deep-love-the-story-of-a...

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Wow, some great reads listed here. Hope you have some luck in finding something entertaining. Here's a few more. have fun
http://ecx.images-amazon.com/images/I/51C9RH7ZPSL._BO2,204,203,200_PIsitb-sticker-arrow-click,TopRight,35,-76_AA240_SH20_OU01_.jpg
Dreaming Pachinko by Isaac Adamson
Singular Rebellion by Saiichi Maruya - (set in the 1960s)
The Tale of Genji by Shikibu Murasaki
Kitchen by Banana Yoshimoto
Underground: The Tokyo Gas Attack and the Japanese Psyche by Haruki Murakami
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