The man was found about 4:30 a.m. after an all-night search by Tulalip Fisheries, the Snohomish County Sheriff's Marine Services Units, and a Coast Guard helicopter, the Sheriff's Office said.
His identity and cause of death will be released later by the Snohomish County Medical Examiner's Office.
A woman in her 40s was rescued from the bay but the man she was with was still missing after their 10-foot boat overturned, Coast Guard officials said.
Police were notified just before 10:30 p.m. that people were in the bay and witnesses could hear someone screaming for help.
Emergency crews responded to search the waters near Potlatch Beach in the area of the 900 block of 43rd St. N.W.
The woman, who was holding a life jacket, was pulled from the water about 40 minutes later. She was rushed to Providence General Hospital in Everett.
She was suffering from hypothermia and is expected to survive, according to the Sheriff's Office. The woman who is believed to be from Mountlake Terrace, had been listed in critical condition late Friday night.
Only two people were in the boat.