By far the best Mexican I've had in Tokyo, and even better than many of the places in San Diego where I'm from, is a tiny place called El Comal. It's on the Toyoko-sen, you can use Shinmaruko or Musashikosugi station.

http://www.elcomal.net/

I've had a lot of the "Mexican" places in Tokyo (La Jolla, Fonda de la Madrugada, Junkadelic, El Torito, Zest, etc) but they don't come close to El Comal.

The Japanese owner lived in Los Angeles for a long time, and learned to cook Mexican there. His menu is pretty authentic, as you can get cabeza (head meat), lengua (tongue), and other types of tacos. No sesos (brains) though There are also a few Tex-mex menu items such as nachos. He also makes some outstanding moles, caldos, hand made corn tortillas and pies.