The text explicitly states that they were the two sons of the miller and his wife. Remember Reek showing Theon the wolf brooch that had belonged to Bran? Reek told Theon, quietly, about the mill. Theon remembered that he'd had some fun with the miller's wife, and that the family had two boys the same ages as Bran and Rickon. Theon then told his men, "I know where they are." Later we are told that those were the two boys he killed and whose heads Theon put on the pikes.