I think it was the NY mob, Frank Costello reputed to be his partner. Actually, I originally read that he had a certain territory and they the rest as “mutually” agreed upon.
Joe Kennedy certainly had dealings with Frank Costello. But I think he did his liquor smuggling in Chicago. None of this is absolutely certain, and it never went to a court of law.
Here’s one article that suggests Chicago ties to Sam Giancana as well as NYC Mafia ties:
http://gangstersinc.tripod.com/SamMomoGiancana.html