There's a relatively new trend called bookstore tourism... which, as I understand it, is organized bus tours of book lovers to cities with a large number of independent bookstores. It's becoming quite popular... there's even a National Council on Bookstore Tourism. I find this very interesting, and am glad to see independent bookstores getting new and appreciative patrons.
I've always practiced my own (and far less formal) brand of bookstore tourism.... I try to find an independent bookstore wherever I travel and go visit it. The Book Sense website is a good place to find listings of bookstores across the United States... just type in a city or zip code to find a bookstore.
I've listed some of my favorite independent bookstores on the right hand side on this blog. Chances are, if it's on my list, it's either a children's bookstore or it has a great children's department. There may also be a few specialty bookstores like The Drama Bookshop, which doesn't have any children's books, but is a holdover favorite from when I used to work in professional theater.
Let me know what your favorites are, and I'll add them to my list (and I'll visit them the next time I'm in the area).