Percy is the son of one of main three gods Annabeth is the second generation of Zeus which equaled in Athena which then equaled in Annabeth Percy has more strength and in one of the books he dared to piss off Thalia Annabeth wouldn't do it Percy relies on strength and since he is a closer to the big 3 then annabeth is Another <- one away
So I believe that percy is stronger
Because in the first book, he beat Annabeth in his first battle! Annabeth has lots of experiences and Percy still beat him, also Percy's dad is god of sea who is one of the main 3 gods! That's the reason why I think that Percy Jackson is a better fighter !
There are two parts on fighting. One being the clever strategy and the other being strength. Percy only has one of those features; strength. On the other hand, Annabeth has both strategy and strength. If you read carefully in the books, Annabeth is told to have swift attack movements, great defence poise and great stealth and agility. Whatmore, Annabeth also inherits great wisdom and strategy skills from her mother, Athena. It gives her a fast and clever strategy even in the midst of the battle itself.
Percy is too compulsive and attacks on instinct, being careless and easily outsmarted in battle that could lead to serious infury and defeat.
Percy relies on brute strength most of the time, and sometimes that's not enough, as Annabeth says "even strength has to bow down to wisdom sometimes". Plus Annabeth is a master strategist, who would be able to make a plan and take out anyone including Percy Jackson. She has been fighting since the age of seven.