There was a newer atlas available for a brief time, but it had the lifespan of a moth, and I can no longer find it even on Amazon.jp. It was like the Tokyo City Atlas, only newer.
I think it is significant, however, that Amazon.jp offers literally dozens of monolingual Japanese-language atlases of Tokyo. The place is confusing even for Japanese people!
But there's no reason to be afraid. Japanese people tend to be kind and helpful to foreign visitors, and street crime is rare. If all else fails, look puzzled and say "Eki (pronounced "ecky")?" and someone will point out the direction of the nearest train or subway station.