As much as I love JNH's Water Horse I think Trevor Jones score is more sweeping, mysterious and adventurous with a slight regional flair.
Yeah, I'd go with Trevor Jones' effort -- though it may not be as impressive as The Dark Crystal it still has that same dreamlike evocation of fantasy, with memorable themes and a broadly epic scope.
Water Horse for me. Loch Ness just sounded like second rate Dark Crystal from what I remember (or maybe that was Dinotopia?). The JNH is a bit overlong on CD, but I've got a nice 30-40 minute whittle edition that suits me fine.