I have an album of pictures of both stores so you can compare and if you search the archives you can find posts comparing the two.
The NY store is a little bigger. Street level has the concierge desk, store exclusives, AGT and Coconut and the bookstore. The second level has historicals and the theatre (I think), next is an in between level with coat check and bathrooms. They used to have a display of paintings of the book illustrations but I don't know if they still do. Third floor is Bitty, Angelina, Hopscotch Hill and the cafe.
I liked the layout of the NY store better. It seemd less jumbled than Chicago. I have not been to the NY cafe so I can not compare that with Chicago but I know the decor is a little different.
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