The name "chocobo" derives from a Japanese brand of chocolate malt ball by Morinaga, ChocoBall (チョコボール, Chokobōru?). The mascot for this product is Kyoro-chan (キョロちゃん?), a bird who says "kweh".
食う / くう / kuu is a rough way to say "eat", whose volitional casual form is 食え / くえ / kue ("let's scoff 'em down!"), leading to Kweh!
Usage
See Special:Whatlinkshere/Etymology:Chocobo for a list of articles using this term.
This is an etymology page: a page detailing the origins of terminology used in the series in regards to real world culture and history.