Harte, I think you're giving Gongora et al. a bit too much credit in saying the "findings then appear to still be in dispute."
I suppose that is true on a basic level, but Gongora et al. are showing a common pattern of ignorance displayed by geneticists who attempt to branch out into archaeological discussions, namely in completely disregarding contextual dating, which in this case included both artifactual assemblages and thermoluminescence dating of pottery. This is seen in their reply to Storey et al.'s reply:
http://www.pnas.org/...05/48/E100.full
Clearly they lack a basic grasp of archaeological methodology.
But Storey et al. were also more kind to Gongora et al. than was warranted, and continued to gather more data re: isotopic analysis to confirm their original findings that the El-Arenal chickens needed no correction for marine dietary sources. This was published as a chapter in a book concerning the topic of Pre-Columbian contact:
http://books.google....=PA139&pg=PA162
I've linked to the part of the chapter that specifically deals with Gongora et al., which unfortunately isn't fully displayed thanks to the restrictions of Google Book previews. The chapter also gives more detailed discussion of the site and stratigraphical context of the finds, demonstrating clearly the security of the dating even without carbon dating. The chapter, except for the specific response to Gongora et al. was reorganized and published as a journal article, available in full online:
http://www.academia....r_their_origins
In the discussion of the archaeological excavation, the stratigraphy is detailed, with three layers yielding evidence of human habitation. All of the artifactual evidence from these three layers comes from pre-Columbian cultural complexes, and there are no artifacts associated with European contact, making it clear that the site was abandoned prior to European contact. In addition it should be noted that the chicken remains were recovered from Layer B of Level III, which is the second layer bearing evidence of human occupation (the first being Layer A sitting directly above it). So it is clear that the chicken remains are older than the most recent pre-Columbian inhabitance of the site.
The rest of the article concerns chicken DNA and morphology in an attempt to trace the origins of the pre-Columbian chicken remains. To paraphrase, the basic conclusion was that the heavy trade of chickens and widespread practice of cross-breeding in the past two centuries means that modern DNA studies as undertaken by Gongora et al. are completely worthless as tools to trace the ancient spread of chickens, and thus typing must concentrate on ancient remains. This bolsters the idea that the El Arenal chickens were of Polynesian origin, though unfortunately does nothing to prove it with certainty given the wide geographic spread of chicken haplotype E1 evident even in older remains.
And leaving chickens behind for a moment (yay!), the above article mentioned another line of potential evidence for pre-Columbian Polynesian contact:
http://www.academia....ON_MOCHA_ISLAND
This article deals with human remains found on Mocha Island in southern Chile which appear to show morphological affinities with Polynesians. Several skulls were studied, with one in particular showing strong cranial affinity. This particular specimen had an artifactual assemblage characteristic of the El Vergel culture, dating 1000-1500 AD, the same cultural complex in which the above chicken remains were found (and the El Arenal site is around 100km to the north).
Definitely another interesting find, though the cranial affinity could be coincidental. Hopefully they'll be able to open new excavations on the island to find more evidence of any contact.