I've always thought guys like Sandman, Hydro Man, Molten Man, and Electro were his deadliest foes. He can't beat them in a direct confrontation without some sort of plot-device/exploitable weakness.
Doctor Octopus. Spider agility/strength is virtually useless against those arms.
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By what metric? Actual number of kills? Total power? Against Spidey specifically or in general? There's also the question of where we draw the line of who's in his rogues gallery. He's fought most of the Marvel universe by this point.
Idol mentioned some with the most potential. But Carnage has racked up more kills than all of those combined. And someone like Morlun probably has the most raw power.
Then there are those that could say the more Prep Versions of the Villains could be more dangerous for their planning and ability to devise some thing that can cause major devastation.
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Well he has beaten ock physically many times. I went back in the old issues and remembered how physically dominant the lizard was. Spidey would hurt his fists punching Connors and he no sold the shit out of him.