Amirthaa is a cheap, clean, pure-veg South Indian restaurant in Bambalapitiya. The place gets pretty hectic, but the food is good.
Shanmugas is one of the older and more reputed vegetarian Indian restaurants. They're definitely pricier than most places but the food is very good and the service is excellent.
Mathura is a decent Indian vegetarian restaurant that has been around Colombo for years, but now at a new location.