After watching the movie I would conclude it's the Spino. To introduce us to it, lowly.

The answer is obvious, the reason we never saw the killer, it was John Cena.

That could be. But it couldn't have been anything as sizable as a T-Rex. There wouldn't have been anything left.

so maybe he was killed by a large predator and then the compies scavenged the body.

The body was picked clean; a sizable dinosaur wouldn't be able to do that, but compies would. Compies alone wouldn't make Eric run off; he'd stay and battle the things - plus the victim's legs were bitten off. Raptors probably would've ripped the guy out of the tree (and chase Eric down), so it was probably a single predator (besides the compies).

interesting theory, what makes you think that out of curiosity?

I always figured he was attacked by compies, then something more sizable came along causing Eric to flee.

We really never find out what killed Ben either do we?

Right.

and there were fresh human remains in the nest with the baby Pteranodons.
Against stupidity the gods themselves contend in vain (Isaac Asimov)

I always assumed it was the flying reptiles. Previous posters disregarded this theory due to them being caged, but the cages were torn up. The reptiles were able to come and go as they pleased, but used the caged area as nesting grounds.

No Spinosaur ! Even if it goes into water they were not built to go out to sea. And how would a Spinosaur been able to climb those cliffs to enter the water in the first place? It had to be flying reptiles!

It was 4 juvenile T.rex's. They actually shot the sequence, and it looks awesome, but in the end, Spielberg felt it was too ferocious and left it on the editing room floor.
A few of the earlier printed laser discs of the film show it as a special feature.

The Pterasaurs from TLW were able to fly free because they weren't migratory. So unless the boat sped past their nest sites then it wasn't them. The mutant Pteranodons in JP3 were imprisoned because INGEN knew they were globe fliers/migratory and so could not be released. So it definitely wasn't them. The boat was travelling too fast for the Spinosaurus to catch. So it wasn't him/her.
The best explanation is the smaller Pterasaurs from TLW and the boat must have sped past their rock nests causing them to attack Otherwise chalk it up to another plothole like the dead ship crew in TLW.

I always assumed it was hit by a flying dinosaurs. The way it tugged on the rope was suggestive.

I think it was those terrible
Dactyls

Jack the Ripper. John Hammond found a way to bring him back through the technology of cloning. They found some "DNA" with one of the prostitutes he killed. After JP closed, his clone has been running around the island in his cloak and top hat. He has since murdered 4 Velociraptors, 2 Dilophosaurus, half a dozen Gallimimus and a big ass T-Rex. He left cryptic clues for Scotland Yard at each of the crime scenes.

I have to agree with your comment. The boat was travelling to fast in open water for the Spinosaurus to eat the people and still leave the boat travelling at speed to keep the parasailers aloft and the dragline taught. Your idea of the aquatic prehistoric creature would make the most sense as those creatures could easily disappear back underwater and also keep up with the boat while eating the people onboard.

The boat was in deep water and travelling too fast for it to be the Spinosaurus. This scene was probably supposed to be foreshadowing for the Pteranodons that appeared later. But if I had my way, it would've been foreshadowing for an aquatic prehistoric creature like a Plesiosaur, Mososaur, or Lipleurodon.

Not if it snatched them right off the boat.
I know, it doesn't make much sense either, but clearly the filmmakers were going for shock-factor rather than making sense.

IF it was the spino wouldn't the ship be sunk?!?!?!?

Actually, it very much was, using capitols and yelling a lot really does not help you either! It was very clear that it was the same family group of Tyrannosaurs, with the baby walking on the very same island.
"Who knows what evil lurks in the hearts of men?"

THE FINAL SCENE OF THE LOST WORLD WAS JUST A POIGNANT SCENE OF DINOSUARS IN THEIR NATURAL HABITAT WITH RICHARD HAMMONDS RICH, GRANDPA-LIKE VOCAL TONES DUBBED OVER.
IT WASNT A GOD DAMN LIVE SCENE FROM ISLA SORNA.
"What is that thing you're using?".. "It's technical."

Thanks! Yes I actually am a big fan of that story, and I appreciate your familiarity with it! Your assertion is interesting, but really, they were both supposed to be Pteranodons, however Jurassic Park 3 retconned a lot of the animal appearances (including Brachiosaurus). So in the end, I fear I have to disagree with you, and honestly doubt they put that much thought into the third film. Still, it would have been a far more interesting angle and story point that could certainly have improved the film overall.
"Aw Crap!" - Hellboy