I don't know if this is contemporary enough for you but this is my favourite book on Tokyo: Tokyo Underworld - Robert Whiting
It's apparently non-fiction but even if it's embellished it's an amazing read that really explains how areas like Roppongi developed in the post war period. Probably one of the best books I've ever read.
Adding on to this if you wanted to read a book on the historical aspect of how integrated it all is, check out Tokyo Underworld. I had to read it for one of my seminar courses and boy was it a bit telling. The Yakuza are involved in so much.
How crazy are you (still) about pro-wrestling? Does it extend to Japan? [eg. Riki Dozan & this book which reveals much of his life including his ties with organized crime and his North Korean heritage ]
Tokyo Underworld, nuff said.
http://www.amazon.com/Tokyo-Underworld-Times-American-Gangster/dp/0375724893