I never thought Vito changed the name himself, although he probably wanted to. It was changed by the FBI and LE when Valachi revealed information about LCN. I believe whichever boss was running things at the time, had the family named after him. And Vito happened to be in charge in 1963.

Joe Profaci was a charter member of the commission, and ran his family for 34 years. But the family is named after Joe Colombo, who took over the family just months before Valachi's testimony. If Valachi flipped a year earlier, the family may have been known as the Magliocco family, after Joe Magliocco. If Valachi flipped two years earlier, it would be known as the Profaci family.

Supposedly, Joe Massino tried to change the name of the Bonanno family to the Massino family, but to no avail.