Quite possibly The Engineer (from The Authority). Iirc, besides counter-hacking Midnighter's tech implant, she also "hacked" Cpt. Atom's biology at the quantum level. And she's a couple steps below Cyborg Supes in overall power.
Speaking of Cyborgs, though, Nu52 Cyborg is probably in the discussion. He's hacked the entire Bat-computer (among many, many other things), yeah? Maybe some of the brainier Transformers as well.