natto or hatcho miso in NYC?
If you do decide to go to Mitsuwa, come hungry. The food court, which was completely redone about 2 years ago, now has some really good options. The ramen is really, really good. They also have other very good alternatives too. And, while you are there, you can pick up you Hatcho miso and natto - they have many options.
IMX, Chinatown, at least in Manhattan, is generally not a great place for most Japanese products; non-assimilated Chinese rarely seem to buy them and turnover is low.
Natto is one of those things I try to pretend doesn't exist (joke !) so I can't help you there, but hacho/hatcho miso is pretty readily available at any Japanese market and IMX, most Korean ones, too. And it's even available at a lot of health food stores these days, though personally I avoid those on low-turnover grounds as well. I think I bought my last pouch at one of the Sunrise Marts, but Katagiri always has it as does Han Ah Rheum. The m2m on 3d Ave probably has it, but I don't recall actually looking for it/seeing it.
I have no idea if Whole Foods carries it, probably, but I wouldn't buy it there (see above.)