Is, or was?

Is. There have been more new threats but who is the greatest threat in the Critical Role universe?

If the question is who is the greatest threat, Ludinus wins by default for being the only active threat.

Obann, Lucien and the Chroma Conclave are all dead, posing no threat to anyone. All that seemingly remains of the Briarwoods is the ghost of Delilah and Vecna is safely behind the divine gate posing no more threat to the universe than any other betrayer god.

That's exactly where I came down. If the question is, "Who has been the greatest/most powerful threat?" then I'd vote Vecna, but if we're going with present tense we have to stick to folks who are actually alive and/or free to act.