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It is unknown what really killed the boat driver. The crew disappears in the mist. There are some uncanonial sorces that give some clues about what happend.

Jurassic Park III Trading Card 2:

"But tragedy strikes when a monster in the mist 
below kills their boating pilot."

Jurassic Park III Film Script: Scene 110:

At the beach Grant asks Eric:

"Eric, do you know what happened to the boat? that brought you here? Why did it crash?"

Eric doesn't know, but they find the speedboat. In the boat the cabin is surprisingly intact, just a little blood. There are three gashes on the driver's seat back. Grant measures their spacing with his fingers.

Grant looks down to the wet sand around him, finding a trail of three-toed tracks.

Grant YELLS at the first chopper, trying to wave it away. But the noise of the blades is DEAFENDING.


At the treeline, the upper branches are shaking. At first, it looks like it's just the wind off the chopper, but something more is happening.

A PTERANODON flies up out of the trees, the first of twenty. It's a gorgeous and terrifying sight.

Probably in the original draft of the script the Pteranodon's were ment to have killed the crew.