I mean, what better souvenir for a trip than a book? I can’t think of one, personally. Bookmarks from those stores are also great souvenirs, and, without even realizing it, I’ve been collecting independent bookstore bookmarks (from Skylight Books in Los Angeles, Brazos Bookstore in Houston, and Dussman das KulturKaufhaus in Berlin as three examples) for several years now (and so, now, make it a point to get one at each bookstore I visit). Looking back at these books and bookmarks makes me inordinately happy, I can tell you.
I have a collection of at least 20 bookmarks from NYC indies.