So what really happened to Tony at the end?
Who clipped him?
will likely never know with certainty. I believe the creator left it open ended in case of a sequel movie or something (sadly Jimmy died), with STRONG contextual hints that Tony was shot.
now obviously the members only guy was the trigger man but the mastermind would’ve been NY/Butch with some assistance/go ahead from who would be remaining of the Jersey family (Patsy and Paulie). Paulie was always snaking around and Patsy had reasons to hate Tony too (Tony had his twin killed). These two would easily be manipulated and forced to conform or merge interests further with NY/Lupertazzi family since at this point jerseys big earners and hitters were all dead. Paulie was never a big warmer and patsy never was powerful or ever above rank of soldier.
NY/Butch gave the ok to hit Phil but if butch was that big of a snake to his own family what makes anyone think he wouldn’t double cross Tony, a man butch never showed any respect towards?
in the end, Butch had the most to gain...have Tony do the dirty work to take out Phil so now butch can head the family as well as having Tony taken out to absorb Jersey (which was NYs plan all along before Phil died).