In Japan, natto is an everyday staple food for a significant portion of the population, so many different natto manufacturers compete for grocery store shelf space. Supermarkets generally carry both national and local brands, but most of these are pretty similar in taste and all packaged in a standardized way-- stacks of three or four single-serving flip-top styrofoam boxes.
Foodie heaven can be found in the giant food halls (depachikas) located in the basements of nearly all department stores. In these markets, an amazing variety of exquisitely presented specialty edibles are sold and free sampling opportunities abound.
In depachikas, "artisanal" natto from small-scale producers are available; many of these are packaged in more traditional, eco-friendly ways and show more noticeable variation between makers--in quality, taste, freshness and packaging.
As is true for any food, fresh high quality natto is much more delicious than the cheaper, industrially-produced version. Premium natto created by artisanal producers is made from carefully chosen soybeans, sourced from small (GMO-free) farms for their particular breed- and climate-dependent flavor/nutritional profiles and bean size, all of which can affect the progression of bean fermentation.
The best kinds of natto are generally produced on a small scale, may only be available in a local area and are delivered fresh without ever being frozen. Natto is a living food containing live probiotic bacteria. Freezing and thawing natto kills most of these microorganisms and also negatively affects its taste and texture. To preserve all of its best qualities, New York Natto will always be fresh and alive, never frozen before sale.