Percy stomps unless Magnus has Jack. Magnus’s only powers are healing and the Peace of Frey thingy. Neither are going to help him to much. Percy’s got his water (which can heal him) and is pretty good with a sword. Those things can actually do something to Magnus.
Even with Jack, it would still depend. I think Percy could be on Jacks level, but I’m also biased. Even if Percy can’t keep up, he has his water for long range. No way Magnus could win by himself.