Okay, I haven't been to Bonaire, but after doing my first liveaboard, I'm hooked! We actually were contemplating this same choice for next year, and decided on the liveaboard, hands down.
For me the liveaboard takes the edge everytime over land-based diving, if diving is the #1 thing you want to do. Once you get on the boat, you unpack and set up your gear once. The routine after you get up in the morning is: eat, go to a dive briefing, gear up, fall off the boat....repeat as desired. Not only will the boat usually move during lunch so you dive 2 sites a day, but depending on the itinerary, you may be going to sites where dayboats can't, which gives you a more pristine reef, and you'll be the only boat there.