Aburiya Kinnosuke or En Japanese Brasserie for something higher end. Both take reservations.
Sankaku is a new sake bar from the owners of Sushi Azabu. Excellent and very reasonably priced drinking snacks and food.
Hall is a new project from the former chef of Kajitsu. There’s a hidden, res-only kaiseki-style restaurant in the back but the menu at Hall is very well executed: it’s a very tastefull fusion of American and Japanese bar food.
Sakagura has probably one of the best sake lists in the city. Two locations: east village and midtown. I like the food menu in midtown better. They also own Decibel in the east village, a more bar-bones sake bar in a basement. Great atmosphere!
Hope that helps!