I believe because JFK's dad was obviously in the bootlegging business,as was LCN.
Once Chicago and NY got their grips into the Prohibition money, they told JFK's dad what HE MUST pay them....He probably was not up to date on what he owed them BUT, claimed that once his son became president, THEY would be paid back in a way that only a President can do. I would guess that THEY wanted pardons for jailed members. Maybe even a re-entry for Lucky.
JFK could NEVER grant a pardon as such in the beginning of his term. Impeachment city!
JFK couldn't deliver on the promise his dad made to LCN....So, they chose to make Sr. feel the most pain. Burying his child.
My theory!
1)JFK should simply ignore Mafia but he made his brother U.S. attorney general that pushed Hoover to fight the mob;
2)Luciano was out of games and was replaced;
3)Of course JFK couldn't keep his father's promises but he not only fight the mafia,made fail the bay of pigs operation,He stood against the military because he don't wanted to attack Vietnam,so made more enemy that friends;
4)pardon the mobsters ? in the 1960 the mob controlled the politicians so, no one could try the impeachment.