Through a corrupt FBI agent, named Doug McCane, Anthony Casso had 14-15 government witnesses whacked before trial. I believe the majority of these people were ratting on LCN, not necessarily Casso or the Lucchese family. It was simple: he'd get the names of the rats, and they would be murdered quickly.
The one instance where the rat received a pass, was when Casso gave the name of Peter Savino to Chin Gigante. The Chin didn't act quick enough. Even after Chin was warned, Savino proceeded to wear a wire and obtain damaging recordings.
Ironically, despite having McCane in his pocket, Gaspipe got nailed in the Windows case with Peter Savino doing the most damage. Chin, too.