If you have an applicable movement speed1, then there's nothing in the rules that states you can't take a 5 foot step.
Flying Maneuver Fly DC
Move less than half speed and remain flying 10
: "I think the rules clearly state that this would fall under the DC 10 'Move less than half speed and remain flying' category."
Careful examination of 5-Foot Step Rules:
Take 5-Foot Step
You can move 5 feet in any round when you don't perform any other kind of movement. Taking this 5-foot step never provokes an attack of opportunity. You can't take more than one 5-foot step in a round, and you can't take a 5-foot step in the same round that you move any distance.
Assuming you don't "fly" anywhere else, except a "5-foot step" directly upward, or diagonally upward, I don't see a problem here.
You can take a 5-foot step before, during, or after your other actions in the round.
Seems you can, while "hovering," draw a potion as a move action, drink it as a standard action, and take a "5-foot step" directly upward, or diagonally upward. I don't see a problem here either.
You can only take a 5-foot-step if your movement isn't hampered by difficult terrain or darkness.
Unless there is severe weather or winds, and you aren't prone to some sort of darkness difficulties, I don't see a problem here either.
Any creature with a speed of 5 feet or less can't take a 5-foot step, since moving even 5 feet requires a move action for such a slow creature.
Unless your fly speed is 5 feet, it seems you can take a "5-foot step" without any rules violations here.
You may not take a 5-foot step using a form of movement for which you do not have a listed speed.
If you have a fly speed, it appears you should in fact be able to take a 5-foot step within that means of movement. Since you would have a fly speed, even with a fly spell, then a simple fly check of DC 10 would allow you to take a "5-foot step" worth of flight.
1You may not take a 5-foot step using a form of movement for which you do not have a listed speed.