Tokyo isn't short of amazing eateries, but often it's a little challenging finding more whole food type options.
Here's two of mine:
1) Coincide in Shibuya
They have a cheapo friendly fish or meat dinner plate for 1280yen, comes with brown rice and copious amounts of organic salad.
2) Kirara in Nakagemguro
Great for lunch or dinner, fish or meat plate with a choice of "deli" side dishes, brown rice, soup and often a "micro" dessert.