It depends on the store, but for the most part the Pirates sets were put on clearance. This means that when they're gone, they're gone. High traffic stores like mine sold out of this stuff a week or so ago. If you know of a lower traffic or more rural store, you might still get lucky and find them. I bought Black Pearl and Captain's Cabin on a Thursday morning and they still had a few other sets. When I got back to work Thursday night, they had sold out of everything but the Pearl and the Captain's Cabin =( Toys, esp. legos, go fast when they are on clearance unfortunately.
You might also try Target or K-Mart if any are in your area. Since the Pirate stuff is old news now, a lot of the big stores are trying to get rid of them. I know that my local Lego store isn't even carrying them anymore.
edit: you can order online and Walmart does free site-to-store shipping (so you can pick it up at your local store) but then it's not on clearance...
Edited by Algus, 16 June 2012 - 12:37 AM.