In no particular order, here are my top five stationery stores in New York City, which you shouldn't miss the next time you visit.

CW Pencil Enterprise is located on Forsyth Street on the Lower East Side.

C.W. Pencil Enterprise. The newcomer to the New York stationery scene opened this spring, after previously operating online-only, and already has been written up in the New York Times and New York Magazine, among others. The shop is tiny, in a good way, meaning that it is carefully curated and every product featured in the store was personally chose by the owner, Caroline Weaver. I am primarily interested in writing with pencils, but there is much to interest the artist as well. The selection of Caran d'Ache (high-end Swiss pencils) is second-to-none, including my personal favorite, the Caran d'Ache Swiss Wood. The store also carries a wide variety of notebooks, sharpeners, and books about pencils. I could spend hours here (which unfortunately was impossible this past weekend).
Kinokuniya Bookstore. A Japanese book and stationery retailer located on the western edge of Bryant Park. While the majority of Kinokuniya is devoted to books and magazines (both English and Japanese), the store also has a phenomenal stationery department, including an entire wall of Japanese notebooks and paper, an aisle devoted to fine-tipped ballpoint, gel, fiber-tipped, and brush pens, mechanical and wooden pencils, erasers, and a few novelties. Even if I don't buy much, or simply browse for an hour, I visit every time I am in town, without fail. Since Art Brown Pen Shop closed down a couple years ago, Kinokuniya is also one of the few options for fountain pens in New York City.
McNally Jackson. A popular, if pricey, independent bookstore in SoHo which also has an office supply branch around the corner. If you can afford them, the office supply store carries some beautiful items. The bookstore has a "stationery nook" that stocks various high-end journals and pocket notebooks, including the limited edition Baron Fig Maker Edition, which I immediately grabbed. In the past, I've had decent luck finding rarer "colors" editions of Field Notes stocked here, but couldn't find the elusive "yellow" version of the Field Notes Two Rivers Edition.
Blick Art Materials. I always visit the Nolita and SoHo outposts of Blick when I'm in town. They carry a great selection of pencils, colored pencils, pastels, paints, and other art supplies. They also have a huge selection of sketchbooks and notebooks from Moleskine, Rhodia, Semicolon, etc. Prices are competitive, and they will order anything for you if they don't have it in stock. DaVinci Artist Supply is another great one, but I don't find myself there as often.
Fountain Pen Hospital. When I am in the City during the week, I try to make the trek down to the Financial District to visit FPH. The last dedicated fountain pen store in New York City, it has occupied the same space since 1946. The store is fairly large, carries both modern and vintage pens, and offers pen restoration and repair services. The selection of ink is also very good. Closed on the weekends, which is a bummer.

A shot of Kinokuniya's "Gel Pen Aisle".  Never seen anything like this in the states, have you? — A shot of Kinokuniya's "Gel Pen Aisle". Never seen anything like this in the states, have you?