This past year, I've done quite a bit of Japanese food sampling both in Japan and in New York. New York has a ton of great Japanese restaurants. Everything from expensive sushi to cheap izakaya style food. There are two places in Manhattan where you can find a plethora of Japanese cuisine - Midtown East (East 40's and 50's) and the East Village (E 10th aka "Little Osaka" and St. Mark's Place). Both areas boast not only fantastic ramen, izakayas and Japanese style curry, but also authentic Japanese grocery stores. Here's a list of some of my favorite spots. I'm guessing I'll find comparable if not better versions once I move to Tokyo:
Cafe Zaiya :: 42st btw 5th and Madison - Cheap lunch to-go and a sweet bakery. I've written about Zaiya's black sesame soft serve before, but their savory food is great too. You can get a hearty and tasty meal for under $6 which is unheard of in NY. I like the spicy chicken sandwich, the mabo tofu and the salmon onigiri.
Dainobu :: 47th btw 2nd and 3rd - The closest thing I've seen to a Japanese "kombini" or convenience store. There are some groceries, candies and some hot/cold food to go. I used to stop here on my way home from The Japan Society twice a week for an easy dinner. I prefer their Ebi Tempura Onigiri but it is on the salty side.
Menchenko Tei :: 45th btw 3rd and Lex - Simple Japanese restaurant with a modern design. Great soups and noodles.
Sunrise Mart :: 10th Street and 3rd - This is probably the best place for Japanese restaurants. They have authentic products from Japan plus all the fresh ingredients you would need to make a traditional Japanese meal. There is another Sunrise Mart in SoHo.
Yakitori Taisho/Oh! Taisho :: St. Marks btw 2nd and 3rd - I don't think there is a different between the two restaurants, but there is a thai lounge separating them which is weird. The wait can be long as this is a pretty popular place amongst J-Expats and NYU students. It is worth the wait - grilled meats (yakitori) and wonderful small plates to share. I highly reccommend the Saikoro Steak which is buttery and melt-in-your-mouth good and the Potatos w/Roe Mayonaise. Kewpie Mayo is up there with Sriracha in terms of awesome condiments from Asia.
Curry-Ya :: 10th Street btw 1st and 2nd - Okay, so actually, Go Go Curry is my favorite curry place in NY but it is on 36th and 8th Avenue which would totally debunk my "East Side" theory. Curry-Ya is on the expensive side for a food that is typically pretty cheap in Japan. They do it well and jazz it up so you feel like you're eating something refined, but at the end of the day, it's just curry and rice.