Dave Malki at Wondermark presents the Stoakes-Whibley Natural Index of Supernatural Collective Nouns, and in so doing performs a valuable service for a worried public. So many confusing and embarassing errors might have been prevented through the timely use of Mr. Malki's comprehensive and accurate reference.
(Via Making Light.)
ETA: Other dragon-related collective noun suggestions include flight, wing, weyr (from multiple sources), doom, blaze and horde. None of them appeal to the same degree as the definitive Stoakes-Whibley answer.