Suffolk County police said the pilot, Joseph Cannizzaro, was trying to fly the plane when the pontoon and left wing caught the water, causing the sea plane to crash into the water at about 6:45 a.m.
Peter Williams took cell phone video as he helped rescue pilot Joseph Cannizzaro.
"Are you tied or not?" Williams said in the video.
Check out this video from Williams, who was on a boat trying to help the pilot (**WARNING: Video sound contains profanity**):
Williams says he was lying in his bed in the morning looking out at the Great South Bay watching the small seaplane.
"And then he crashed right in right down," Williams said.
Williams flew out of bed and got into his boat.
"I jumped right in the boat and that's when I called 911 at the same time that I'm trying to get out and get out to him," Williams said.
About 1,000 feet off shore he reached Cannizzaro who was calmly waiting on his flipped over plane.
A witness showed Eyewitness News a picture of Cannizzaro backing his plane into the water using a pickup truck around 6:30 a.m.
Jack Stevens says he was fishing around that time and also saw Cannizzaro struggling to maintain altitude.
"He was floating along there for a little bit and then he turned like he was going to take off again, and as he took off again I think the wind caught his upper wing and tipped him and the other wing hit the water and he flipped over," Stevens said.
Suffolk Marine Bureau officers were finally able to pull the plane to shore.
Williams says it was a good team effort.
"You're happy you could help?" Eyewitness News said.
"Oh definitely, definitely that's all you can do is try to help somebody," Williams said.
Eyewitness News tried to reach Cannizzaro, but he didn't return our calls or messages.
The Coast Guard says he refused medical attention at the scene.
The sea plane was towed to a nearby beach. The FAA is investigating the incident.