Just as it's nearly senseless / impossible to name one or two of Paris's best venues for coffee/tea, it's silly to try to pick one bookstore of Paris's myriad variety as my favorite or the 'best'. Situated in the Latin Quarter, along some of the other most remarkable bookstores (in addition to the corporate behemoths Gilbert Joseph, with whom I have an appropriately French relationship of love/hate), Librairie Compagnie stands out for its interesting selection and regularly fascinating events (highpoint: seeing Rancière present his new book on the evening of my birthday). It's not architecturally grand or quaint - rather modern in fact, so if you're searching for a Shakespeare & Co type romantic bookstore, you're out of luck. But if you want to browse a fascinating range of books (in French) or drop in on a reading, this place is one of my top suggestions. Others: L'Arbre à Lettres & Tschann.
If you're looking to window shop, avoid the Champs-Elysees and the Rue de Rivoli and dive into the Marais. There's literally everything here and while in the height of tourist season(s) the streets can reach the point of annoyingly-overflowing there's always a side street or alley to duck down into and explore. I've spent years aimlessly wandering these streets and I continue to find amazing things tucked away in corners.