This is just my breakdown of character intelligence from what i've read over the years;
Aside from cosmic entities, I'd say Doom is the most intelligent overall, as he is second only to Richards in science and second only to Dr Strange in Magic. Reed would be second, but not too far off are Apocalypse, the High Evolutionary and Doctor Strange. The Leader could well be at this level. real world geniuses at this level would be Gottifried Liebniz, Leonardo Di Vinci, Isaac Newton, Ludwig Wittgenstein and possibly Physicist Edward Witten who developed M-Theory and won the fields medal in mathematics, as well as Andrew Wiles, the Mathematician who solved Fermat's last theorem. IQ's 180>
Below them are Stark, Banner, Octavius, Xavier, Pym, McCoy - High IQ's, perhaps to the level of real scientists such as Stephen Hawking, Carl Sagan, Murray Gell-Man (who entered Yale at 15), and Michio Kaku (who built a particle accelerator while at high school and graduated Summa cum laude from Harvard). World-renowned figures in their fields.
Below them are genius or near-genius characters such as Peter Parker, who is written as precociously bright and perceptive. I would say the Punisher would rank at this level. He is a keen strategist, and regualrly takes on superpowered foes with conventional weaponary.