What about when the AI is in the air? How can I make 3D nav meshes?

You can’t make a NavMesh for stuff like that. If you had aircraft flying around you’d use a completely different system. A NavMesh is meant for ground navigation. There’s too many variables for a NavMesh to work in the air. If you were really inclined on this you could use an aerial object that’s directly connected to the movement of an object (invisible) utilizing a NavMesh on the ground. You’re still going to be limited to the variations of the ground though.