West Nile virus?
One article speculated the following:
The birds showed physical trauma, said Rowe, who surmised that “the flock could have been hit by lightning or high-altitude hail.”
The agency also said another possibility is that New Year’s Eve revelers shooting off fireworks in the area could have startled the birds from their roost and caused them to die from stress.
http://www.msnbc.msn.com/id/40874105/ns/us_news-environment/