Yes, so long as you can see it
The description of misty step (PHB, pg. 260) says:
Briefly surrounded by silvery mist, you teleport up to 30 feet to an unoccupied space that you can see.
So long as you can see the point in the air that you wish to teleport to (and it's no more than 30 feet away from you) you should be able to teleport up to it, and your flight speed from being an Aarakocra or from being affected by fly should keep you in midair.