During an after trial meeting, the bosses decide to eliminate anyone involved or with knowledge of the skim in order to keep them from testifying.
The car bombing wasn't authorized and Nikky was the one responsible for that, so why was Sam spared by the bosses?
Because Sam was their top earner and with the change in casinos after their trial, they kept him around to keep earning. He had already proven himself during his previous trials about his license and not only that, he survived the bombing. This had two implications, first is that he wasn't like Nicky and the second, he had far too much press after he survived the bombing as he was the center of attention with the gaming board. They really couldn't kill him without proving they (the bosses) were involved.
Because Sam still can see the angle: He has deep knowledge of the underworld, He understand how gambling world works. For this understanding he still can earn lot of money and most of all he can send money back home to Bosses. Well, no bosses will will kill a golden goose.
Besides Sam never betrayed the bosses. You see even when Nicky tried to persuade him to take over but Sam refused to be part of that. Another thing that Sam directly didn't help to skim the casino. He just made absolutely sure that the casino earns money. So I think Sam couldn't be a witness and he is not considered as a threat.
