I work down in the same area, and have been looking for the past year and a half. I would agree with David's comments, and add that my favorite these days is Delica in the Ferry Building. It is very clean/healthy, yet tastes quite authentic (I lived in Tokyo for a couple of years and ate a LOT of Japanese food there ;-)
I'd recommend their various bento boxes, the curries, and the noodles, in roughly that order. The tonkatsu is decent, and all of it is uniformly high quality.
Ozumo is a nice business lunch sort of place, but more expensive, and often too noisy for me.
What kind of Japanese? There's cheap lunch sushi at Kamakura on Battery or, much better but farther, Mikaku on Grant. Kyo-ya is expensive and upscale, and Ozumo is hip and creative. Cafe Tomo on 1st has some Japanese-inspired items, though I don't like it as much as others do.