You'll find all those chain stores and more going up and down 5th ave. All the way from Soho to midtown is nothing but shopping.
I don't really bother with the cool, hip, NYC boutiques and things like that because they are too expensive. I don't know what your budget is like, but you could try places like Olive and Bette's, Intermix, Purdy Girl, and Built By Wendy--all are great stores, but over my price point. Buffalo Exchange is a vintage/consignment store but you can find some amazing things there (so I hear).
I have noticed that few people who visit NYC ever really venture outside of Manhattan, which is a real shame because you can find some great stuff. I lived in Brooklyn for four years and adored it. If you don't mind hopping on the subway and making the trip, Williamsburg (the Bedford Avenue stop on the L train) is a treasure trove. There are a few great vintage stores in the area. Beacon's Closet is my favorite. There is another one that is probably a 5-10 minute walk down Bedford but I don't remember what it is called. The whole street is lined with cute little shops (not just clothes but books and music...one of my favorite bookstores is in that area). Cog and Pearl is also a great store. I think Fred Flare also opened a brick and mortar store in Brooklyn but I don't know if that is your style.
For shoes, I think Union Square is probably a good spot to look. There is a Shoemania and DSW. I'm sure there is a David Z close by too (there are David Z's all over NYC).
For department stores, I have a soft spot for Lord and Taylor. We don't have a Nordstrom and most of the other dept. stores are either too overwhelming (I'm talking about you, Macys), or too pricey. I think they are really the most underrated department store in the world. Their website is fairly unimpressive and doesn't even have half of the in-store stock, but that just makes it even better to shop in a real store.
I could go on and on about this, but you'll only be here a few days :p
On a separate note, I hope you find some relief from your tendinitis! It sounds awful. I know I'm just days away from some computer-related ailment.
