A lot of people. Tony was despised by the time that show ended. It could've been Butch, after giving Phil's whereabouts up after being assured he'd be boss and things would be swept under the rug once Phil got hit. It could've all been a double cross and Butch could've had him whacked anyway to take over Jersey. Remember Butch never liked Tony, and I never got the impression he feared him either. Could've been someone loyal to Feech La Manna, he could've made the call from prison. Could've been Furio, could've literally been anybody.
I considered the scene to be a fictional version of Anthony Caponigro being double crossed after receiving the green light to kill Angelo Bruno.
In addition, Leotardo's hit was probably not commission sanctioned, so somebody had to pay. However, in real life, there would have been a sit down with Tony and some commission representatives, I believe. And Tony wouldn't have been clipped while having dinner with his family.
