New York City Serenade - S3-E12
Plot hole: When talking to Hook about the photos, Emma states he could have photoshopped them to make it look like she and Henry were in Storybrooke, however she had taken them directly from Henry's camera and had them developed. So Hook had no way to photoshop the pictures from inside the camera. (00:27:00)
Answer: He knows who she is because he knows that the fairy tales are true. He was also shown to sneak out to go see Emma or someone else. Sometimes he succeeded, sometimes he didn't. This is how he knew to look for her despite his strict mother.