The boomerang isn't stunning the alligators in World 2 Zone 1 at all. In the first rivers it passes trough the alligator and hits the turtle. a little further down the zone, after the raft. when you have to use the flowers to jump forward there is another alligator. trying to hit it with a boomerang clearly shows its passing trough the head, but not stunning it.
This image shows the boomerang inside the mouth of one of the alligators, and yet, it will not be stunned at all. This was the case last year as well