When the Skulls members are heading out to the island, the castle in the background is Singer Castle on Dark Island. The island that the Skull and Bone Society owns is called Deer Island. Both islands are in the Thousand Island of the St. Lawrence River.
When Chloe is being chased, she runs out of a campus building, across the Yale Bowl, and into another campus building. In reality, the Yale Bowl is located a few miles from the main campus.