The forerunners where the strongest. Think about it. The Covenant might win by sheer numbers, the forerunners had factories that could produce a centennial every 2 seconds, AND they had 9 rings (Halos) that could destroy all life in the galaxy (exept them, they had a safehouse in Onyx that was immune to the rings). Forerunners win.
Next hunters are by far the strongest warrior. They are huge (over ten feet I think), they have almost indestructible armor, and a big ass cannon strapped to thier arm. I've got my money on the hunter. Although Spartans are far more effective, the hunters would win in a fistfight.