I've always had great times at Hinomaru:
http://www.hinomarukanko.com/ It's in Kabuki-cho, Shinjuku. They also have a coupon offer for Y2000 off on the website, and they frequently distribute said coupons about two blocks away from the place.
One of the few places in Tokyo which accepts everyone. Japanese-speaking gaijin can get into maybe 30% of the places, maybe more if they have a good connection. If you're not Japanese, Asian or white, your chances are few and far between, but I've always thought highly of Hinomaru.