Hi,
I've been to both, too, and each has its charms. Basically, it comes down to your deciding whether you want to do self-guided shore dives, the special aspect of Bonaire, or guided boat dives on Little Cayman.
The one piece of advise I would give is to not dive Grand Cayman--it's over-dived and not at all interesting. The only night dive I ever did where no fish showed up was off Grand Cayman! However, there is one kinda touristy dive we did off Grand Cayman that was fun: Stingray City. If you want a safe, fun, up-close-and-personal experience with stingrays, this is it. However, some folks object to it because it is "artificial" and may create an overly man-made sea environment: the stingrays are attracted to the site because they are fed by divers and snorklers. I still enjoyed the experience.
joewr