I'm not sure how PCOS actually relates to your son being born without a thyroid; and yes, PCOS is an endocrine condition. So is your thyroid part of the endocrine system.
Do you have thyroid issues yourself? PCOS and hypothyroidism often go hand in hand.
Like Barb says, can you tell us if you were tested for a hypothyroid condition prior to your pregnancy. In answer to some questions both on this board and through our foundation, we have found a site that helps explain why birth defects can occur when the mother is hypothyroidic at time of conception:
http://www.ivf1.com/hypothyroidism