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)
Plot hole: To wake Mr. Gold/Rumplestiltskin from his coma, Emma needs an object that touched him before he became the Dark One. Hook shows her a sword, telling her how he held it to Rumplestiltskin's head and taunted him. However, the sword that Hook shows to Emma, is not the sword that he threatened Rumplestiltskin with in "The Crocodile." The sword that he used to threaten him had a unique, golden handle. When Hook and Rumplestiltskin met again a few years later, Rumplestiltskin took the same sword from Hook and dueled him with it. When Rumplestiltskin vanished into thin air after cutting off Hook's hand, he took the sword with him. The sword that Hook shows to Emma, which Emma uses to wake Mr. Gold, has a black handle with a completely different design, and is the sword Hook carried after the other one was taken from him; he can be seen using it in episodes like "Queen of Hearts", "Lost Girl" and "The Jolly Roger." This means that the sword Emma uses to wake Mr. Gold from his coma never actually touched him at all; however, the spell still works.
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.