Gardy is faster and more powerful, but after Gallade has flipped all Prizes, the G&G can do a maximum of 60 damage which isn't enough to stand against Magmortar. Even to the Non-Lv.X Magmortar it's not a 2HKO without PlusPowers.
If Magmortar is played with Typhlosion, Psychic Lock can help to avoid getting swarmed, but it's still very difficult. In my opinion, Magmortar has the better matchup, but there's not much difference, something about 55-45.
The reason why Gardy wins more tournaments is because its only death matchup in the current metagame is T2 Banette, but nobody plays T2Ban any more because it has autoloss to Magmortar. On the other side, Magmortar has bad matchups vs any water decks like Hurricane and Empoleon, which are still played enough to be taken serious.