If you like more secret place, try Rogetsuan or Nioka, next best but ones of top in Japan.
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This is a top of top soba restaurant, Sango-an in Shirogane. Even listed in Micheline, lunch cost you from 800
Good authentic Belgian restaurant in Shinagawa St.
Sushi Tatsumi at Ginza 8-5-19 serving same tast of Michellin 3 star at less than $100 and open until 2 am
If you are in the mood of Chinese, go Osho of Gyoza (Dumplin). 1,000 yen will satisfy you including beer on tap.