I also believe Tony was whacked, and the reason was most likely Carlo. Remember, he was going to flip, and that could've triggered a domino effect that would've ended up hurting the New York bosses. What if Carlo's testimony was so damning that it made Tony himself flip? Gangsters don't generally like to leave stuff like that to chance. If I was the New York boss and I heard that a high ranking NJ guy was flipping, I'd start cutting all ties too, starting with Tony, the biggest tie.