My current go-to coffee shop in the West Village is The Elk (128 Charles Street) because there's no place quite like it. The scene is super earthy - there are freshly cut flowers placed on each table, amazing products for sale (such as my favorite sea-salt hair spray from Herbivore Botanicals) and the food is delicious and uses local ingredients.
The Elk's decor reflects founder (and Vancouver native) Claire Chan's "chill Northwest style," infused with wood and white tones, with cozy cushions to sit on. The scene is very relaxing and the staff is friendly and upbeat. They brew Parlor coffee (based in Brooklyn) and have an extensive menu--I recommend the SOFT SCRAMBLE (Cage-Free Local Eggs, Sweet Potato Hash, Roasted Tomato) or the OATMEAL (Steel-Cut, Rolled Oats, Cinnamon, Nutmeg, Almond-Coconut Crumble.)