I've been lucky over my 30 years and only had one really nasty hive - it was filled with burr-comb though "because" I did a lousy job of handling frames back then, so I probably asked for it, prevenative maintenance can make a huge difference.
I'm not sure what more to suggest - requeening is a real option that might settle them down, is the hive over grown and seriously brood bound (relative to food and brood balanced mix) I know heavy brood is often a good reason for overly protective bees.
If I had the equipment and I was you, I might think of splitting them, the queen will end up somewhere, and with brood around in the other half of the hive, they'll make a new queen - then 1) see if the hive with the queen settled down and 2) see if the new queen has a gentler nature. If "2" is true, the taking and raising a new queen from her eggs might tame the original hive - but the whole issue here gets down to WATERING DOWN the DNA with DRONES from other hives.
You could just as well kill off the queen in the hive that is giving you problem after raising a queen from a hive that is gentle in your yard, introducing that queen into the hive and HOPEFULLY the next generation of bees will be milder.
The problem often goes back to poor pheromonal scent which always controls behaviour in the colony. If NONE is present then the bees are mis-guided and lazy, if some scent is present, but NOT ENOUGH to control behaviour fully, then the bees are unstable in their mood - often causing OVER REACTION to the beekeeper's intervention.
Just killing off the queen really only weakens her strain if non-related drones mate with the reared virgin queen - I think it better to raise one separately, and as stated above kill of this nasty hives queen, introduce the new one AFTER MATING using queen cages (extending the time she is sealed to at least a week) they'll build and destroy queen cells as her pheromone is accepted.
All the while, the hive will NOT have enough time to replace the killed off queen on their own - make sure if you did do this that NO QUEEN CELLS are present when you kill off the queen, you don't want competition with your replacement queen.
It's just a shame they are being so nasty. I was in the yard today with my neighbor, me in shorts, him with his usual beer in hand slobbering over my frames (better a happy drunk than a nasty one I guess) and all three hives were as relaxed and carefree as nature allows. He was even poking a hand at them trying to pick out drones and not one went airborn after either of us.
Often, it has NOTHING TO DO WITH US, it's good breeding and the luck of the draw when ordering them. It sounds as if you do everything right and to have THOUSANDS AIRBORN is just not right - I don't think I'd keep that hive around if AFTER changing queens and letting a generation of bees come and go AND STILL they are nasty - at that point, I think I'd have to do drastic measures and drown them out. It's a terrible thing but living in a neighborhood as I do with kids nearby and neighbors whos car is only feet from the hive, I'd have to either find a new home (best solution - some field where they can be nasty all they want but serve as good pollinators) or kill off the hive to stop that nasty streak in its tracks.
Good Luck Queen Bee - keep us updated.