The piece I posted from the Sun Tabloid is sort of a follow up or companion piece to the NYT article which is challenged by the Scientific American article you posted.
Not sure what to believe, because according to this excerpt from SA:
The world already knew that plenty of smart folks believe in alien visitors, and that pilots sometimes encounter strange phenomena in the upper atmosphere - phenomena explained by entities other than space aliens, such as a weather balloon, a rocket launch or even a solar eruption.
Huh?? Upper atmosphere????
Here is an article from the NYT which clearly states, and shows video from "50 feet above the churn" (in the ocean, definitely not the upper atmosphere):
Hovering 50 feet above the churn was an aircraft of some kind — whitish — that was around 40 feet long and oval in shape. The craft was jumping around erratically, staying over the wave disturbance but not moving in any specific direction, Commander Fravor said. The disturbance looked like frothy waves and foam, as if the water were boiling.