Ill take your nuke and raise you 1 planetary collision.
What people fail to see is that it's "Nature" and not "Planet Earth". Things like tornadoes and earthquakes are mere scratches. When you talk about nature, things like asteroid collisions and supernovae come into play. Then, it's not even a question.
Asteroid 1 mile in diameter will wipe out most life.
Bio weapons, nature's deadliest weapon made stronger by humans.
Most natural things do not last long for example tornadoes, or large storms, excluding earthquakes, and things from space. But a nuclear weapon would have a long lasting effect on earths environment like making water undrinkable, or making high radiation levels killing plants and animals causing mass extinction.