Sky Lords Series by John Brosnan

Centuries in the future, after the world has been devasted by the Gene Wars, the scattered remnants of humanity struggle against both the spreading biological blight on the ground and the great airships that dominate the skies. Controlled by feudal warlords, these mile-long dirigibles patrol their territories, exacting tribute from the ground communities.

1st edition paperback, vg++

This final volume of "The Sky Lords Trilogy" finds Jan Dorvin encased in an underwater cell, the prisoner of the sexually indeterminate Eloi. Far above, the struggle against the mighty airships continues, as Ashley, a rogue computer personality, once again joins forces with Milo Haze.