Those little islands off the shackles, with towns named Quent, Ollo and Drenchport seem like the best options. Since some interpretations of Freeport have a nearby city starting up (Libertyville), one of the other towns could be that new community.
Putting it in the place of Quent would require the least work, although I'd want to tweak the island to be larger and include some rainforest, to better suit the actual Freeport island appearance.
You could also have it appear on that island north of the Eye of Abendago, and replace Ilzmagorti with Freeport. In that case, the island already has some jungle and 'works' as drawn, and you might want to either fold in the concept of the Red Mantis Sect (adding it to the local cults and societies crawling around Freeport) or move the Red Mantis' to another location (such as Quent, Drenchport, etc.).
It really depends on whether or not you want to use all of Golarion's available 'stuff.' If you don't care for the Red Mantis stuff, Ilzmagorti is perfect. If you don't care for the 'Impossible Kingdom of Jalmeray,' that island is also pretty neat (although perhaps not perfectly positioned for a pirate haven, being too close to potential retaliation from large nautical powers). Even if you do want to use Ilzmagorti as Freeport, and still use the Red Mantis Society, you can move the Red Mantis' to another location (perhaps they hide within the Screaming Jungle?), incorporate them into the cults & societies of Freeport, or replace completely one (or more) of the other cults & societies of Freeport with the Red Mantis sect.
I did something similar porting Freeport into Greyhawk, having a Scarlet Brotherhood presence, so Freeport's pretty easy to squeeze into other settings, IMO.