I'm assuming that this only includes species which we've actually seen piloting ships. I'd say the Douwd, if we include his hologram ship from "The Survivors." I think that ship could take as much energy as the Douwd could, and I doubt any starship could produce that.
If the Douwd isn't included, I think the Krenim, Species 8472, Kelvans, and Tosk would be some of the hardest to defeat. Possibly the Borg also.