As a resident of Tokyo, I think some of the other reviews have been overly critical of this restaurant. Indeed, it's not the easiest location to find but the reality is that running a vegan restaurant in Tokyo is more of a personal dream, rather than something profitable and thus it often simply isn't possible to open shop in prime real estate areas.
That said, I used to work nearby and frequented Nagi Shokudo for lunch. I believe they have a curry plate and some kind of daily lunch plate in addition to the choose 3 lunch plate (additional items can be added for a fee). I usually got the choose 3 lunch plate in which you are able to choose 3 deli items from a list of about 10 and those are served with salad, brown rice, miso soup, and a drink for 1000yen. A dessert can also be added for, I think, 250yen. I wouldn't describe the portions as large but they are adequate and still more than some other vegan cafes in the Shibuya area. Everything I had there was always quite good and fresh-tasting. In response to another review, I find that the amount of oil used in foods is significantly less than what you would encounter in a restaurant in a typical Western country.
However as some people have pointed out, I agree that lunch at Nagi Shokudo is better than dinner. It's not that the quality is bad; rather, the dinner menu seems like lunch-size portions at dinner time prices. The last time I went there for dinner, you could order a la carte, the dinner course, or the dinner set, which was basically the same 1000yen lunch set. If you do go for dinner, I recommend getting the 1000yen set and splitting some a la carte items.
All in all, I think Nagi Shokudo is a lovely option for a vegan Japanese lunch, but if you are looking for a large-portioned, cheap dinner, then here is not the place.Pros: nice selection for lunch, freshly made, good vegan miso soup
Cons: might be hard to find, tables are abnormally small