I'd go with the Borg as well. Based on what we've seen in the Stargate series (especially Atlantis), the Replicators are really easy to manipulate once you can get at their base code. The Borg assimilate everything and basically reprogram it. See where I'm going with this?
Eh. I DO see your point, but as a baddie, I think the Replicators have been totally underportrayed in the show. Don't forget, they damned near destroyed the Asgards, who can be argued, are more technologically-advanced than even the Federation. They even actually destroyed most of the Ancients, who were definitely more tech-advanced.
I think the writers just had to find a way to beat a basically unbeatable foe. The way they did it is with the unorthodox methods humans employ (by necessity, considering we didn't have half the toys the Asgards and the Ancients had). The more head-on methods the other races employed didn't work.
This is where I think the Replicators have been totally held back on what they can potentially be. Considering that even the most complicated viruses can be mostly stopped by a free anti-virus program, I find it underwhelming that a human hack can be so easily spread between trillions of separate entities (each replicator block). Even then, the Atlantis team has the advantage of having the knowledge of the creators of the Replicators at their disposal. Kinda like having access to the MS Vista developers' notes and codes, to create a hack.
We can safely assume that the Borg will employ head-on tactics to subdue the Replicators. While the Borg is busy attempting to reprogram the Replicators, the Replicators are slowly eating away at their ship and bodies, making new Replicators out of them.
I think one of the Borg's greatest weaknesses in this fight is that they have organic parts that can die.
Another thing is, they have made the Replicators basically stupid and overconfident on the show. Now, think about this. The Borg might have their Queen, but now the Replicators have Dr. Weir.
Don't get me wrong. I don't think it's a slam dunk for the Replicators at all. I just think it's a lot closer than you think.
PS: The Replicators' ships are faster.
