Since this poll is in the FFX forums, clearly Sin is going to win the poll. Even if it wasn't, though, I'd still say Sin would win. If there was a battle between Sin and Vegnagun, there's a chance Vegnagun would destroy Sin if it managed to get a shot. However, this doesn't mean Sin would stand idle and wait for Vegnagun to shoot. Vegnagun is a big machine, and it can't really move much, so it can't dodge attacks whereas Sin can move and fly around.

Sin could send Sinspawns and powerful attacks to kill those who are controlling Vegnagun or use some attack to jam Vegnagun's weapon controls. I don't think Vegnagun would stand a chance in a battle, only in a cheap ambush shot against Sin.