The vessel overturned in the waters that separate Manasquan and Point Pleasant Beach at around 8:30 p.m.
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First responders rescued two people and spent the day Friday searching for the third.
Surveillance video caught what appears to be a wave knocking the boat over.
Witnesses say the two men who were rescued held onto a cooler to get to safety. They were taken to an area hospital to be checked out.
There was a small craft advisory in effect at the time the boat overturned.
Captain Bob Dogan, who runs a deep sea fishing business, had to cancel tours Saturday due to the rough waters.
"We haven't been out the last few days because of the weather, we know our limits," Bogan said.
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Waves were 8-to-10 feet high on Friday and were only expected to get worse over the weekend due to Hurricane Lee.
The storm is expected to cause dangerous conditions on beaches up and down the shore.
U.S. Coast Guard crews are asking people to give the rescue teams the time and space to do their jobs.
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