How about Dojo-nabe?
Dojo nabe is loach hotpot. It's a traditional Tokyo dish! You can try at Komagata Dozeu in Asakusa or Shibuya.
Also Monjayaki is a Tokyo local dish. It's like okonomiyaki in Osaka but they use dashi broth and really tasty.
Some other Tokyo's local food are listed here:
Balloon fish (fugu) and whale. Domestic beef such as kobe /wagyu beef chicken sashimi.