YouTube dropped that vid. But judging by your description of it, I have to assume it was the Randy Johnson fastball that hit that pigeon as it flew by right in his path. That was something else.
I noticed the clip disappeared as well, due to copyright violation or something. But that was the one with randy johnson's fastball crossing path with a bird.
The only other time in MLB that a bird was killed by a baseball was during a throw around warm up. Dave Winfield who was with the yankees at the time (i think) struck a bird with a baseball and knocked it dead. He got arrested after the game. PETA accused him of animal cruelty and attempted to file charge against him. Of course they were laughed out of the room and handed the hat.