Sushi, Tempura, of course. I hear many travelers saying that sushi and tempura in Japan taste much better. (One of my friend said about Tempura: "Tempura in the U.S., batters dominate the taste. But in Japan, I discovered this was the dish to taste the ingredients. I can taste what's inside the batter in Japan")
I'd like to recommend Japanese sweets, wagashi.
There are various kinds but Taiyaki is one of my favorite. It's a fish shaped pancake like sweets having red bean paste inside. It's very tasty!
Visiting a local Izakaya, Japanese pubs, and order a couple of Yakitori grilled chicken skewers and edamame. You can find many local Izakayas in Ueno, Shibuya, and Shinjuku. Hit Nonbei Yokocho in Shibuya or Omoide Yokocho in Shinjuku. There are tons of Izakayas creating great smells in tiny streets.
Also, from my experience, Japanese snacks are the best in the world. Go to any convenience stores and supermarkets and grab few bags of chips and chocolates. You will be amazed by the taste!