I am a huge Bonaire fan, so much so that I go there every year for a month. But, I have to say, Little Cayman's Bloody Bay Wall diving is superior to anywhere I've ever been in the Caribbean. You see big stuff there, as opposed to Bonaire, where you'll not see many big grouper and likely will never see a reef shark. But, it really isn't fair to compare the two. Bonaire is so much about the experience of choosing your own dive site and time, being the author of your own day. Little Cayman is like most other dive spots - you dive when and where they take you. But "where they take you" is unbelievable!
Also, in my experience, Little Cayman is more of a social experience than Bonaire. Each of the 4 (maybe 5?) resorts there is small and offers all-inclusive, family-style dining. You dive with, eat with, etc. the same people, basically, all week and, if you're like me, come away having made lasting friendships. Now, that's not for everybody, but it really added to the enjoyment of my vacation.
I think you should promise yourself not to miss either one. But, since you're planning to go in October, I'll echo what everybody else is saying. Go to Bonaire; eliminate the hurricane worry.