Sin. But only because FFX was so much better than FFX-2.

Vegnagun may have had the power to destroy Sin, but it would never have done so, since it is a sentient Machina, and could not distinguish between User or Foe. Not only that, Summons always own Machines with pianoes on them.

If you want to think about it in gaming terms:
Sin requires the X button, thought, and maybe, JUST MAYBE, the D-Pad.
Vegnagun will somehow die, even if you unplug your controller and play Warcraft III.

Vegnagun will have died within five minutes.