Sometimes when the hive is destroyed the queen will just fly in place. If you have a quetzal or a Tapejara you can fly up to it and passive tame it right there. I recommend bringing medical brew just so you don't have to worry about the drones. Make sure to feed your tame bug repellant as well.
ALWAYS break the hive with ranged attacks. If you choose to melee it,drones will continuously spawn from it infinitely, and they will repair the hive, so best to shoot it down and kill all the drones before attempting a tame. Oh, and the queen will spawn more drones periodically, so bee careful.
Easiest way : go to ab then look for the hives , the hives stack so destroy all hives with a mana or whichever tame you have then the bee will be stuck in the hive , what you can do is is get an angle on the bee and easy tame while its sitting