Honestly. The Borg. The Reapers don't even really come into play, the Borg are just too advanced.
The Sovereign Class Reaper's main gun puts out about 400 Kilotons per second (And appears capable of one-shotting most ships.).
The Photon Torpedo of the Federation is 64 Megatons. And is usually fired by volleys the Borg ignore without Superbald Captain or SuperPMS Captain.