The SoHo area where Kee's is located (and I heartily second Carol's recommendation, btw) is one of the neighborhoods in the city where it is possible to hit a number of different chocolate shops on foot in close order.
On Broadway (corner of Spring or Prince) is Dean and Deluca's where you'll find one of the better selections of bars in the city. Not far from there is Vosges. Kee's is on Thompson just south of Spring (#80) and if you head down Thompson away from Spring and turn left on Broome in a block or two you'll find Marie Belle's.
From there, it's a 10-15 minute walk to Jacques Torres on the corner of Varick/King.
Down in the financial district you'll find Christopher Norman and further uptown (on 49th I believe) is a Food Emporium that boasts a wide selection, including being the only place to purchase Coppeneur bars at retail in NYC.
In Rockefeller center there is a Teuscher store and a La Maison du Chocolat boutique.
On the Upper West Side it sometimes pays to wander in Fairway and Zabar's. I once saw bars from Oriol Balaguer in Fairway. They were under a checkout counter, not in the aisle where the chocolate was displayed so it really does make sense to explore.
Please let us know what you find out on your trip and post photos and make a photo album.