Sorry krcollins
The cheapest way is to do it yourself. Otherwise you're paying your percentage of the travel expenses for those:
divemasters for those that want a little additional attention.
Not to mention the diveshop's overhead on the trip. I've always found it cheaper to book trips myself or through an online divetravel agency. I haven't had good luck with either Scuba Sciences Travel or Tierra Mar Travel (El Mar's inhouse). I've even given them a chance to earn my business after I've made firm plans, they've been unable to get within $200 of the price I've negotiated. Either place.
Most of the diveresorts have their own websites as do all the airlines. Some destinations even show up on Travelocity or Expedia, but not the best deal. In addition, it's also sometimes worth it to make a phone call, I was going to book a condo in the Caymans online, but then called their booking office (in Iowa) because I had a question. The agent offered me an upgrade deal - higher up/better unit/ocean view - for the same as I would've booked one with a parking lot view.
All the diveops on Bonaire automatically provide a DM on boat dives. So bringing your own is counterproductive as the locals know the sites better anyway. Nice if you're the DM though...
Read the ABC or Bay Islands forums here for ideas on where to stay, how to get there etc. You'll find lots of divers more interested in getting to the diving than having fancy amenities once there. So just what you're looking for.
Roatan will probably wind up being cheaper but there's more to getting there. Try
Cocoview's website as a starting point. They're used to dealing with newish divers.
Bonaire can be done through Houston direct on Continental on Saturday now. But you have to leave here Friday night to make the connection.
A clean, newer, less expensive place to stay on Bonaire is
Golden Reef Inn. Not on the water - you pay more for that - just a couple blocks away. They put together really inexpensive room/dive/car packages also. I think Liz, the owner will help book your flights if asked. Staying there, you'll want a car.
Some divetravel agencies to look at:
www.aquadreams.com - I deal with Dani there - she's a diver.
www.caradonna.com
www.bonairepros.com
hth,