We went to Bonaire for the first time a month ago. I just finally got the photos uploaded to my gallery so have at them folks. It was my first time with an UW camera so some might not be so hot.
As for boat vs. shore diving, well... it depends. We did four boat dives that came with our package and 14 shore dives and both have their advantages. For the boat diving it was diving off of Klein Bonaire which has some very nice sites, such as Bonaventure.
For the shore diving it's flexibility. Dive when you want where you want, it's all up to you. Too many people at a particular site like the Hilma Hooker, come back later if you want.
They both have their disavantages as well. For the boat diving, depending on who you're diving with, you may get large group of divers on the boat. We were on Jerry's reef when a group from the Divi came through and all I could think of was 'all together now, MOO!!!".
Just kidding, it wasn't that bad, but you get the point.
And the disadvantage to shore diving is schlepping your gear and making entries and exits on ironshore and coral rubble which will require good hard soled booties.
The options are there and either way you'll have a good time.