Ok, I love Percy better than I love Harry, but Harry would kick Percy's butt (even post-Styx Percy) because Harry isn't limited to one element like Percy is, and if its a one-on-one fight then Percy can't get help from other gods or demi-gods. Harry has a lot more material to pull on when he enters the fight. Also, Harry can use the SKY as well as the ground, and Zeus pretty much will strike Percy out of the air if his feet leave land.
I like Harry Potter more BUT I think he would win in a fight because:
a) he's the Chosen One b) he seems to luck his way out of every situation c) he relies on the talents of his friends (who would appear out of no where and help him) d) I don't know Percy Jackson's powers