Man, Bonaire has some great food and there's no reason to sign up for food at just one resort. I'm getting hungry just thinking about it.
I also agree that the boat dives are a waste. You're catch the boat around 8:00 to 8:30 and you're lucky if you get back to the dock by noon for a one tank dive. I would have rather done two shore dives and be in town for lunch in the same time.
If you want to dive Town Pier or Salt Pier, you need the harbormaster's permission. So you'll need to get your dive shop to make the arrangements as soon as you check in with them. I missed Salt Pier because I didn't make arrangements soon enough.
Town Pier is a pretty good night dive, but its still got too many folks on the site for me.
I bought my fiancee an interactive dive with Dee Scarr and Dee took us to Town Pier one afternoon. We got almost 2 hours on the site and there were only three of us on the pier. She knows where all the critters are on that site, and has named most of them. She also shows you a bit about the ecology and environment of the reef. Fantastic. You might could probably get her to DM/critterspot for you if you asked for a trip on Town Pier. Well worth the money, I thought. 
When we went to Bonaire, we stayed at Yacht Club Apts. Basic and cheap, but we only slept there. You'll want/need a truck rental to get to all the sites on the island... and then you'll be diving at your own pace.