It used to be Reed all the way. And counting all his feats he is still well ahead I think. But yeah they have definitely pushed him down a bit in recent years for whatever reasons. I still think Reed/Doom at the top.
But part of the problem is Marvel's shift further and further from the sort of basis in reality that was part of their original formula for success. Back then each genius was limited, and usually they had some special field they were expert in to distinguish them in some way. Now all the geniuses do such ludicrously over the top stuff in any field they like and it's almost impossible to pick who is top. They just do whatever crazy feat is required for plot.
Remember the days when Reed actually stood out? Or when Tony Stark was an industrialist and semi-conventional weapons maker instead of tooling with Dyson spheres and other crazy stuff? Or when Banner was a gamma ray expert and not making Banner Tech force fields and teleporting around? When Pym and McCoy were biochemists and Pym dabbled in clunky robots instead of transdimensional infinite mansions , and Beast wasn't building time machines?
Galactus is probably the best judge of this,and he told Reed he has a universal intellect.Doom is very close to this,Pym and Banner are a notch down to me!