I was a manager at Petco for years. The reptiles at my store were ordered from multiple breeders/wholesalers. Most were captive bred but some, such as iguanas, were wild caught. I would shy away from purchasing a reptile from Petco though because they are typically unhealthy and severely underweight.
When it comes to BP they are farmed hatched (in other words hatch in big pits in africa and then imported) as for the other animals they sell I have no Idea.