James Dahlen Jr., 51, surrendered to authorities on Wednesday morning. He was charged with criminal trespass and faces up to 18 months in prison.
County prosecutor Jeffrey Sutherland said additional charges may be filed.
Dahlen is a mechanic for Paramount Air Services, the banner plane company that owns the Piper PA12. The owner of Paramount Air says the pilot is her stepson, who took the plane after-hours on Sunday night.
Several eyewitnesses caught video of the plane in flight. In one video, the pilot can be seen coming dangerously close to homes and boats along the bay, and even crowded beaches.
People say they thought he was just someone trying to show off, but then it looked like he could crash.
"It looked like it was going to be bad," said eyewitness Kyle Kreisler. "He kept going up and nosediving."
Another eyewitness, Clark Morris, says the plane was "probably three feet above the antennas of my boat. I was ready to jump overboard."
Officials say Dahlen flew farther south, and that just before 8 p.m. the plane landed on the beach inside the secure Coast Guard training facility in Cape May.
At first they say the pilot tried to take off back into the air from the beach but failed. Officers immediately responded, but when they got to the plane, it was empty.
Officials say Dahlen is seen on surveillance video getting out and running away.
The plane wasn't damaged in the incident.