Cyborg Superman vs Brainiac

Let's go with Henshaw, and New52 Brainiac.

If Brainiac didnt suffer a power outage in that version, he wins.

I'm on the fence myself.

On one hand, Brainiac took on Superdoom, a massive Phantom Zone portal, and still nearly beat Earth.

Otoh, Henshaw took over an entire techno-planet and part of the source wall. Hacking the entire Brainiac fleet might not be a stretch..

Ftr, New52 Brainiac actually created their version of Cyborg Superman (Supergirls daddy).

From what you describe, Brainac seems the tougher nerd.