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Given their uncanny resemblance to winged Owlbears on the cover of Guide to Korvosa, I'm going with the assumption that the Academae first produced them via magical experimentation, Owlbears being failed attempts at producing Hippogriffs, or the first step to learning how to produce them, and now supply the Sable Company each year with the produce of their highest ranking students.
I like this idea, because it anchors them to the setting, and puts a definite Pathfinder spin on an otherwise familiar creature concept.

Ross Byers RPG Superstar 2008 Top 32 |

According to myth, hippogriffs are the offspring of a gryphon and a horse.
In D&D, I'm pretty sure that they're a true-breeding, separate species.
I'd assume that the original Sable Company Marines had some hippogriffs for reconnaisance when they came to Korvosa (or were entirely mounted, since flying mounts are still useful at sea), and that Korvosa's 'griffs are the descendants of those. They are ranched in the same manner as horses, save that they need to have their wings clipped as colts to keep them from just flying away.