"Der Akkord" is hands down the best bakery in Tokyo. They are all organic, vegan and macrobiotic. They use only whole wheat flour and natural yeast (Tennen Koboki) and do not use cane sugars. If you don't want each of your items individually packaged in a plastic bag (as is the custom in Japanese bakeries), just say "fukuro irimasen".
Their chocolate an pan is great and I have fallen in love with their fruchenbrockt (raisin and walnut crunchy bread sticks) to the point where I have bought their cookbook and make it at home. Their personal apple pies are pretty good too. Aside from being a stellar bakery, they are great people: Very nice and accommodating.
Cons: A little pricey (but worth it)