From what I can tell, the Borg brainwash you(not really, but something akin to that) which is way more evil and terrifying than just being outright killed; suppressing my free will and using me as a tool to destroy everything I cherish is a scarier notion than just being killed/outbred by the Cylons.
I think the fact the Borg won was right but for the wrong reason. What makes them terrifying to me is that every moment you are transformed you can fell the implants going into your skin and limbs and bodyparts being removed and cut off. Until your mind is locked you feel everything that is happening even the implants being put into your brain and that is truly horrifying.It sort or makes Jigsaw's torture from saw look tame. The Psylons, you're going to die or manipulated which you can recover from but the borg.... even if you get rescued some how. You will never be the same person your were before.
I think the definition of Cyborg needs to be expanded on a bit, because from where I sit cybord needs to be a melding of biological and mechanical which the Borg are and the Cylons aren't, they just fake it really well. IMO it has to be the reapers from Mass effect
^This, which also rules out Skynet as a whole, although the later films do involve at least one true cyborg. I'm not an expert on the canon though.
Also, I think that "biggest threat" is an interesting statement. It could mean in absolute terms - so a "bigger threat" would be the one which could kill more humans - or relative terms - so a "bigger threat" would be more likely to wipe out humanity, or stunt our growth indefinitely.
Finally, people are suggesting the Cybermen as a contender her but I think that's a little pointless given how much more of a threat the Daleks (Who perhaps should have been considered) were shown to be at Canary Wharf