The first Dojo restaurant I remember was on St. Mark's Place. It was cramped, always crowded, tasty and cheap. Not too much has changed since closing the east side location and moving into the larger west side location that used to be a Swensen's Ice Cream Parlor (think that was the brand.)
The menu is still pretty much the same with a really good selection of vegetarian options and wide variety of food and styles in general.
I love the Soy Burgers, Hijiki Burgers, Steamed Veggies and pretty much anything you can eat with their Carrot Ginger Dressing. The salads are good and I understand the other dishes are quite tasty as well. The prices are unbeatable - e.g., The Soy Burger Dinner which is the burger, Brown Rice and Salad for under $6.
The place does get noisy and crowded as its in the middle of NYU and the Village in general but if you go off-peak its not bad and you can almost always get a table as the space accommodates lots of diners.