ISO West Village Bar with Outdoor Garden/Smoking
Hudson Bar and Books has outdoor sidewalk seating in front and patrons can smoke indoors. (The bar offers a selection of cigars. Indoor smoking might be limited to these, technically.) Vol de Nuit also has an outdoor courtyard where they allow smoking. Other than these, I don't know of any places in the neighborhood that allow smoking outdoors in a garden area or elsewhere. I'm not a smoker, though, so I also don't seek these places out.
Vol de Nuit
148 W 4th St, New York, NY 10012
Hudson Bar and Books
636 Hudson St, New York, NY 10014