Pure Cafe is a favourite for me in Tokyo. We've been many times and it never disappoints. Friendly staff, fresh, delicious, healthy vegan food. More Westernized than Japanese style food. Breakfast options include tofu spread or peanut butter on toast, or amazing granola. Lunch options include sets with a drink, soup, rice and a main. Dinner at Pure is the best as there are a few 'deli' choices, or a burger or enchiladas or the vegeholic with tahini sauce which is my personal favourite.
Only a few minutes walk from Omotesando train station, exit B3. A great long walk from Harajuku station (20-25 minutes).
A must for vegans travelling Tokyo!