Libreria Aqua Alta has quickly become one of the most visited bookshops in Venice, mostly by tourists. It has a gondola in the middle of the shop, it's full of cats, has a staircase made of books and a gondola where you could go on for free (now the steps heading to the gondola are damaged, but hopefully they'll fix it soon).
It feels more like a sight to see than a bookshop, and of course it can be pretty crowded, so if you're looking for a quiet bookshop, this is not it. They have several international books and if you don't mind a bit of chaos, it can be a great spot.
They also have super cute tote bags :)