Shohei Imamura (The Eel),
Shohei Imamura (Vengeance is Mine),
Shohei Imamura (Black Rain) and
Nagisa Oshima (The Sun's Burial).
Hiroshi Teshigahara (Woman in the Dunes, Rikyu) and
Seijun Suzuki (Branded to Kill). More
Imamura (The Ballad of Narayama, Profound Desire of the Gods, Eijanaika?!) and even more
Oshima if you can find/stomach it (Three Resurrected Drunkards, Kyoto, My Mother's Place, Realm of Senses/Passion, Max mon amour, Death by Hanging, Taboo).
Oh yeah, and
Juzo Itami too (Tampopo, Minbo, then everything else you can find).
These dudes are all older though. I don't know if any good Directors have come of age in the current generation of Japanese. Those dudes in the 60s rocked (even if they were jerks).
Actually, if you can find it,
Nagisa Oshima did a tv documentary which walks you through the history of Japanese cinema from the beginning through the mid 90s. It is full of excellent/obscure/canonical recommendations. And it's pretty awesome (Oh how I wish I'd brought a notebook with me when I saw it at a festival last fall). It is called
100 Years of Japanese Cinema. It may be an ironic title given some of the stuff Oshima himself wrote/said about nations and cinema but it's a list far more serious and eclectic than I can offer.
There are some good old independent Japanese movies playing in NY in the next few weeks if you happen to be in the area. I plan to see at least 3 of them.
http://www.japansociety.org/shinjuku_ecstasy