Where it lives in the city
Japanese food in New York splits along a line worth understanding before booking. The high-end sushi rooms are scattered through Midtown and Tribeca and run on omakase, where the chef decides and the bill follows suit. The denser, cheaper and considerably livelier concentration is around St Marks Place in the East Village, where izakaya — Japanese drinking houses, closer to a tapas bar than a restaurant — have clustered thickly enough that the strip gets called Little Tokyo, informally rather than officially. Ramen shops sit alongside them, several opened by cooks who brought a Tokyo shop over rather than inventing one here. If you want sushi as an occasion, look uptown; if you want small plates, yakitori and a late kitchen, the East Village is the better walk, and it does not require a reservation weeks out.
Michelin picks
Sobaya
Authentic soba noodles
Near Midtown, right now
Live from OpenStreetMap, filtered to venues tagged japanese within about a mile of Times Square — thin coverage outside that radius, and tagging is crowd-sourced, so treat this as a starting point.
No tagged japanese spots turned up near Midtown right now.