I've seen lots of flags on EBay, also take a look at Mouse Surplus from time to time if you want something park specific.
If you're looking for something to buy actually at Disney World, go to the Disney Marketplace. Go to the Toy Store (the one with the big Mr. Potato Head outside), it is on the northernmost tip of the marketplace, right next to the Earl of Sandwich store.
Go in the store, go to about the 3rd or 4th "room", on your right hand side in the corner up against the wall will be a bunch of Pirates of the Carribean merchandise. They have two flags to choose from, a regular skull and bones and a colored skull and bones that says "Pirates of the Carribean" in small print underneath it.
Ok, so yes I've bought a flag from there and yes I've visited that section too much...lol.