Chaya Macrobiotic was, hands down, my favorite restaurant in Tokyo. The restaurant was very easy to find (it is located on the 9th floor of the huge Isetan department store) and the menu was available in English. The waitstaff were very helpful in checking on the ingredients in some of the dishes for me.
There were a number of interesting vegan options on the menu, including vegetable croquettes (cornmeal dumplings) and vegetable brochettes (sausage-like vegetarian meat-on-a stick, served with a vegetable kabob and three different dipping sauces). The restaurant also had homemade ginger ale, which was extremely refreshing on a humid Tokyo summer day. For dessert, there were a few dairy-free options, including tofu cheesecake and pink grapefruit pie (made with agar-agar instead of gelatin).