Most of us will agree that Venom is much stronger. The symbiote bonds not only to the physical, but the emotional as well. It feeds off of emotions, and amplifies them, particularly the negative ones.
Peter always resisted the black suit, never really unleashing it's power in an attempt to maintain his autonomy. Venom on the other hand, embraces the suit and takes full advantage of it. Venom is the amplification of hate, misery, and vengeance into a physical monstrosity.
In the older comics, Peter could never really beat Venom. He always managed to either trick him, use his weaknesses against him (fire/sound). He even made truces with Venom that they wouldn't attack each other.
Spider-man always truly feared Venom. In my opinion, he doesn't fear any other villain moreso than him, because at one point, it was him. Doesn't trigger his spider-sense, knows everything about him...pretty frightening if you ask me.
But none of that is fully realized in SM3, and poor Venom has gotten the shaft in the newer iterations of him in the comics...
