I would say that my favorite place would have to be Little Giant on Broome & Orchard. It's small, and the menu is not robust but it's one of those places that you cannot get a bad meal at! Plus they have a keen eye for wines from vineyards that you may not know about but will definitely like. Oh and if they have the ginger mojito available get it! My definite recommendation!
I sometimes work near 2nd & B. Two good, affordable lunch spots are the vegetarian Indian cabbie joint (named Punjabi Deli, I think?) near the northwest corner of Avenue A & Houston.... and also Cafe Himalaya, near the northeast corner of 1st & 1st.