If it's still there (every time I go back at least one of my favourite shops is gone) the cookware shop on the north side of 17th Street between Broadway and Fifth (close to Broadway, though), the name or address of which I never remember, had an amazing selection of stock, great prices, and some of the surliest staff you can imagine. If/when you're in the area of Union Square, definitely worth a look.
Broadway Panhandler is impressive, but if you go in with a backpack, they will make you check it
ETA: For actual chocolates, La Maison du Chocolat is literally my third stop every time I set foot back in NYC. I usually hit the one near Rockefeller Center (because there is–or, I hope still is–a Japanese sweet shop nearby, which is my second stop, following Yasuda; also, it tends to be remarkably quiet for the area), although the one further uptown on the west side of Madison between 78th and 79th has a bigger selection (I'm not usually in the mood to schlep that far uptown when I'm still trundling my baggage behind me). I also really like Petrossian's chocolates, on 7th Avenue, between 57th and 58th (do not be put off/convulsed with laughter by the sometimes hilariously would-be-hip staff).