Do you want to look stat wise or plot wise?
Suiko I had Crowley, Luc, and Tengaar with the highest stats, although, right behind them were: Cleo, Eileen, Hellion, Grenseal, Lotte, McDohl, Milich, Odessa, and Ted.
Suiko II had Luc as the sole highest MGC stat at 08.
07 had Mazus, Jowy, McDohl, and Sigfried. 06 had mages like Sierra, Rina, and Tengaar. 05 had mages like Nina, Riou, and Zamza.
In Suikoden III, the highest MGC stat was tied with Luc and Sarah at 08.
07 MGC was tied between Estella, Joker, Sasarai, and Yuiri, 06 MGC was Lucia, Queen, Rody, both Vikis, Yuber, and Yumi.
The strongest MGC in Suiko IV were characters like Maxine, Ted, Jeane, and Warlock. Slightly lower was Viki, Wendell, Conrad, Sigurd, Katarina, Pablo, and the Hero.
Now, if we're going pure gameplay and including every character, I'm going to say Luc. Although McDohl is an adept magician, he simply doesn't have the advantages of learning from Leknaat. Plus, the True Runes are so powerful, and with Luc's naturally affinity with magic, he puts it to devastating use.
However, if I was going to use non-True Rune characters and going plotwise, I would say:
Suiko I: Crowley. He's simply had much more experience then Tengaar or any of the others. The only soldier type cahracters who have experience using magic in combat settings would be Cleo, Grenseal, Milich, and Odessa. None of them are devoted to magery like Crowley was. Besides, Crowley has infused many runes into his body, more then any of them have.
Suiko II: Mazus. Although I would normally go for Jowy, the Black Sword could technically be counted as a True Rune. Mazus also has much more experience then the others.
Suiko III: Joker. Although Yuiri is a powerful mystic, she is still a young woman, whereas Joker has been using magic for neearly as long as she has been alive. Estella is also a pathological liar, and her claims about beating Crowley are dubious at best.