So things Pym does in the backround of his comics...
Pym has collapsed realities(something the entire illumanati couldn't do), built a home in what amounts to heaven (underspace), out thinks Ultron to the point it had gotten embarrassing... Not to mention the many varied fields he holds high level degrees in.
Everything from biology to physics to mechanical engineering to A.I. robotics
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In all seriousness to Lex, I do think his stock rose a lot right before the reboot. He had good feats before to be sure, but they really gave him a much needed push in the last few years of DC's previous canon.
I think the top three would probably be Pym, Luthor, and Banner.
One's mileage may vary. I would say Pym and Luthor are pretty close to one another. Recently, Banner's been getting really good tech feats and direct comparison to peers, but I'd edge Luthor and Pym over him.
That are things that Superman has done, much less Lex. Building a heaven which captures spirits, done in For Tomorrow. Outsmarting Brainiac 13, done in Y2K. Creating miracle machine that recreates entire multiverse, done in Final crisis. So Pym is almost as smart as Superman?
When has Pym ever usurped the power of an omnipotent?
If they ever crossed over, Lex would be a rival to Reed more than Pym. He's just that smart. Pym and Banner are small fishes.
I'd think Lex would be facing off more against the likes of Stark and Pym than Reed. Partly because Reed is more of an explorer scientist than one who's constantly building things like Stark or a (good) mad scientist type like Pym. Not to say him and Reed couldn't be rivals, but Luthor is just as much of a business man as he is a scientist.
Actually, the more I think about it, the more I realize that Luthor and Stark would probably get into the most more so that Luthor with either Richards or Pym.