In Keara's flying fortress, the entrance to the headquarters is almost at the very top, a little below the platform with the wizard tower on it. Fly around the fortress and look for a small, square section of fortified walls, with a teleporter portal in the middle (second highest platform).

Here is a map showing the rough location of the shield generators. They are towers and a nest, though, so easier to deal with than finding the generators in human form in other fortresses.

From the D2:ED walkthrough:
Keara's Flying Fortress [FLKEF]
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Location: south of Champion Harbour

-You must destroy six things to disable the anti-dragon zone.
-Three of them are three lightning towers (west, southwest, and southeast).
-Two are wizard towers (northwest and east).

-The last is a nest tower to the northeas). Be careful when attacking it: it's
actually inside the anti-dragon zone.