I have both, and I use the stability ball, but not the Bosu (which has a slow leak, so if I DO want to use it, I have to inflate it every time).
The Bosu could be good for cardio that is specifically made for it, or for adapting Firm or maybe earlier Kathy Smith-type step workouts. You can also use it to stand on to add a core/balance component to weight work (and reducing the amount of weight used), something you can't (well, not unless you're somebody like Paul Chek!) on a stability ball.
I think that the stability ball and Bosu are actually more different than they seem. Bosu is for strength (standing and supine positions), core and cardio, while the stability ball is more suited to strength (from a supine position) and core.