There are pirates in Scott Lynch's Red Seas Under Red Skies, and they occupy a good bit of the book, though they don't form part of the main plot, and it's the second in the series, so you might want to read The Lies of Locke Lamora (no pirates in that, from memory) first in order to understand some of it.
I'm trying to recall another fantasy I've read which has pirates, but while I'm waiting for my brain cells to kick into gear, I'll move this over to Book Discussion since you're wanting recommendations, not looking for a specific previously-read-now-title-forgotten book, which is what Book Search is for.