A disabled engine stranded the 28-foot recreational boat.
Coast Guard officials say the two fishermen were hoisted from the boat to a helicopter and flown to Paine Field in Snohomish County.
Local agencies were not able to help because the boat was stuck in shallow water. No injuries were reported.
The two men were not injured.
Responders were concerned about the risk of hypothermia due to the cold weather. According to officials, the men had no cold-weather survival gear on board.
"Proper vessel maintenance and preparation are key to survival in winter weather," said Petty Officer First Class Mario Roy, a watchstander at Sector Puget Sound who helped coordinate the case. "If anybody is going out on the water this winter, they should always be ready for the worst-case scenario by taking extra food, drinks, blankets and survival gear."
The Associated Press contributed to this report.