There are a bunch of excellent taquerias in Sunset Park, including Tacos Xochimilco and Tacos Matamoros (both on Fifth Ave near 45th St) and Piaxtla es Mexico, often referred to as Ricos Tacos because of the signage (right off of Fifth Ave on 51st St). It's hard to go wrong at any of them for tacos. Do a search for Sunset Park Mexican for more information on the Fifth Avenue corridor running roughly between 39th and 60th streets, which forms the backbone of Brooklyn's most concentrated Mexican (and Central American) neighborhood.
In North Brooklyn, Bushwick's Tortilleria Mexicana Los Hermanos is well known and now frequented heavily by hipsters, but the place still cranks out pretty tasty tacos.
Other folks on here have provided good information on the whole taco truck scene (as opposed to sit-down restaurants), so do a search for that as well if you're interested.