I'm not a native, but I lived there. That's how I got into mhf in the first place. Unfortunatly, I'm not a traveler. I hate it, in fact. The only places I visited were in Tokyo. One of my friends used to work part-time at this awesome ra-men place in Akiba. Unfortunatly, it's a little place and it's off the beaten path, and while I could get there, I don't think I could explain how to get there to someone else.
Sorry.
I go to Akiba for events, but my choice of restaurant is always KFC. It's convenient and close by to the store I go to. (Plus it has power points so I can play mh while I wait hehe)
The only restaurant that comes to mind is in Ikebukuro, Tokyo. hxxp://r.gnavi.co.jp/g528910/
It's called The Lockup. It's a themed restaurant set to be like a jail and every now and then they turn the lights off and play heavy metal music and guys dressed as monsters run around and try to scare you. The menu is weird in a funny way. The girls wear short skirts. What's not to like? It's pretty easy to find, too. There's a main shopping district called Sunshine Street. It has a movie theater, restaurants, tons of video game arcades, as well as Tokyuu Hands, and the main super mall, Sunshine City. Near the entrance to the mall, on the opposite side of the street, on like the sixth or fifth floor, is The Lockup. You can see the sign from the street.