I've gotta take issue with a few things.
Ok we have an alien race come to harvest humans on a world covered 70% by water...but their weakness is water?
Maybe they enjoy the challenge and sport of it, like the Predator. Besides: they scouted it first...they didn't LAND in the water. They kept to the land. Remember what Ray said? None of the sightings were near water.
They have invisible starships..but dont realize the spectrum of light their ships give off is viewable at night?
Maybe they don't care if they're seen floating there.
They can cross the immense interstellar gulfs of space and navigate to a small planet in a insignificant system...but they need crop circles for landing co-ordinates?
Perhaps it's part of their culture and tradition. Just because they're aliens with spaceships, it doesn't mean they don't have historical customs the way we do. They're not The Borg, after all. They're not necessarily 100% efficient in all ways.
That's my view, at least. There are lots of potential explanations for all this stuff. M. Night chose to leave explanations aside because, in the end, this wasn't about WHY or HOW the aliens did what they did...it was about the family reacting to the situation.