The boat has been recovered, city spokeswoman Kate Reardon said.
KIRO-TV news Chopper 7 pilot Clark Stahl spotted the vessel early Tuesday morning and alerted authorities.
It isn't yet clear what caused the accident, Reardon said. The boat was being kept in an undisclosed location as part of an ongoing police investigation.
Officials believe two men were aboard the 12-foot vessel early Monday afternoon. The water was cold, and waves of up to two feet were coming from the northwest.
A Lake Stevens couple was headed to a picnic on Jetty Island when they found a man treading water and calling for help, they said.
The man, 49, of Everett, was taken to a local hospital for hypothermia treatment. He has since been released.
The second man, the boat's owner, had not been found as of Tuesday evening. He has been identified, but his name was not released Tuesday.
The man's family was at the 10th Street boat launch where officials were staging their search. They asked for privacy.
Crews spent much of Monday evening and Tuesday searching the water. Various police and rescue boats could be seen from shore well into Tuesday afternoon.
Yellow police tape still cordoned off the northwest corner of the boat launch, where local marine law enforcement experts set up their operations.
Investigators haven't said why the men were on the water or whether they were wearing life jackets.
Emergency responders from throughout the region have been assisting with the operation.
Rikki King: 425-339-3449; firstname.lastname@example.org
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