For new books:
McNally Jackson (kinda an obvious choice, always a really good selection, Soho & Williamsburg locations)
Greenlight Bookstore (my local new books bookstore, where I go most often, Fort Greene BK)
For used books:
Housing Works Bookstore (some great finds here, housing works is a nonprofit that fights AIDS and homelessness, they mostly have thrift stores but also this 1 used book shop!)
The Strand (another obvious one but I go here so often too tbh)
Unnameable Books (many people have said this already but want to +1 it! my local shop!)