I think they are equally good. But One Piece storyline is more on a larger scale while Naruto is more about bond and personal relationship. I didn't think the Strawhat crews are really that good of a friend until Foxy Pirate arc honestly. I just feel like they are more like classmate that got stuck together instead of a clique. While Naruto, even though they are classmates, they really are friends. If the strawhats lose their crewmates right after fighting Eneru, the emotional impact wouldn't be as strong as it was.
Naruto's story is just as strong as One Piece. There are many people who accused Naruto of not thinking beyond 1 or 2 arcs, while One Piece, it is obvious the story was planned several arcs ahead. So yeah many can say One Piece is better. But it can't be denied, the whole Itachi storylines, if we go back to read at the things he said in the beginning, and the flashback prior to the end of Part I, and now that we know the truth (including the secret mission), the whole thing just works.
Anyway I think, as far as the plot is concern, they are both good. Better than Dragonball Z's writings anyway. Which other than the ingenious Cell/cyborg saga, I don't think Toriyama planned too far ahead. Don't even get me started on Bleach. (this comment is regarding plot only)