The water turbulence wasn't in the video actually. From the wikipedia article:
"They looked down at the sea and also noticed a turbulent oval area of churning water with foam and frothy waves "the size of a Boeing 737 airplane"[14] with a smoother area of lighter color at the center, as if the waves were breaking over something just under the surface.[14] A few seconds later, they noticed an unusual object hovering with erratic movements at a height they estimated to be about 50 feet (15 m) above the churning water. Both Fravor[15] and Slaight later described the object as a large bright white Tic Tac, 30 to 46 feet (9.1 to 14.0 m) long, with no windshield nor porthole, no wing nor empennage, and no visible engine nor exhaust plume."
So they noticed a disturbance in the water that appeared to be caused by something under the surface, and it was only then that they noticed the tictac object hovering above the ocean. Whatever you make of it, it's very strange.
That link is super cool, but I imagine that if you scaled it up to the point where it produced a uniform plasma orb 30+ feet in diamater (would love to see the napkin math on how much energy this would take), the visible light from the plasma would be blinding, which was definitely not what the pilots described.