Snacky on Grand between Bedford and Driggs is a great stand-by, though it's not entirely Japanese (they also serve Chinese and Korean). The place has a great vibe, well-priced menu, is open late (1am). The Wasabi Shumai and Curry Soba Noodle are delicious.
the crowded korean/japanese place at the corner of N. 6th and Berry is suprisingly good. And the korean influence is a nice bonus, like the kimchee dumplings. For regular rolls, we prefer their spicy cruncy tuna to most other places.
I went to Zenkichi for my birthday last week and had a memorable meal. The omakase for 2 was fabulous...loved everything. Amazing sake list...I tried a tasting of 3 different sakes. No sushi. A very authentic Japanese experience, in many ways.
No good sushi in the burg? can you honestly say you have tried it all? For people who may be a bit easier to please I would recommend Samurai on N. 6th & Bedford. And my personal favorite, Bozu, everything I have eaten there has been very tasty.