Watamula is the boat dive to do. Mushroom Forest is another that's only done by boat. We were actually talked out of Mushroom Forest by the DM - he said that all the coral on coral there makes the fish life sparse since they have nowhere to hide - they took us to a farther away site - Lost Anchor - so I tend to believe him. We liked the Lodge KH also, it's pretty pleasant there - one of the leading small hotels in the world. Their dive is one of the best shore dives also - it's Playa Kalki/Alice in Wonderland. Different in both directions - more vertical to the north.
As you move east there are a lot of good shore dives - the "Gnip" sites, Playa Jeremi, Playa Lagun, Varsenbaai, Porto Mari, all are good dives. Superior Producer the signature wreck is just west of Willemstad also. There's not as much good diving right near town then it gets a little better again east of town - the Tugboat is the other famous site there. The pier nearby is better and the wall around the point is a good dive also. In fact since the boat is only in 20' - do it as a safety stop.
You also can't get out to Klein Curacao any other way than by boat. It's pretty much an all day trip and usually done from the East side. Also any of the East Point dives are boat dives only. We only dove as far east as Tugboat so I don't have any recommendations.
If you wanted to stay closer to town, just about 5 mins. south of town is the SeaQuarium area. The main Ocean Encounters shop is there, they do the Dolphin Dives 5mins. away - the dolphins live at the Seaquarium - and they dive some of the better sites nearby. Lions Dive is a dive resort next to them, it's a little more upscale. Can be done as a semi-AI as they have meal plan options. But there's also several other good restaurants in that area. Next to them is Sunscape - the full AI resort on Curacao - it's an ex-Breezes with another OE shop on-site.
For Bonaire - as mentioned above, Klein Bonaire is only boat accessible. About 1/4 of the Bonaire sites are around it so you'd miss some good ones. Forest was a good dive. But 4-6 boat dives probably covers it. IMO one of the best Bonaire dives - Rappel - is a boat dive only also.
Any of the dive resorts on Bonaire are comparable. Buddy Dive has a lot of fans here. Habitat is just north of it. Both have good house dives but from Habitat you can hit two - Cliff to the north and their house dive - the LaMachaca wreck.
South of there is Sand Dollar and Den Laman condos. They're on Bari Reef, the site with the most counted species of fish in the Caribbean. Both have dive operators - Dive Friends at SD and Bonaire Dive & Adventure at DL. BDA also has a naturalist on-site - his BMP orientation is better than some and they'll dive with you (for a fee) if you want to do a REEF fishcount there.
South of there is Eden Beach, a nicer beach with WannaDive on property. IDK a lot about their dive. As you move closer to town from there, generally the diving isn't as good. The Divi is south of town - probably the only dive resort that you can walk to downtown from. South of there is the Plaza - a larger resort with Toucan Dive on-site. It's a sprawling property with the dive shop/boats on one end and their shore dive on the other. Not as convenient as the north side resorts.
South of there past the lagoon and airport is Belnem. There are some options there also but about the only dive shops are the Dive Friends location at Port Bonaire or the Buddy Dive Shop at BelMar Apts. - there's one more but I can't recall where. Dive Friends has about 5 locations on island for tank exchange etc. Most rental properties in that area - houses/condos etc. also have a dive package deal with someone. Usually some sort of on-site storage facilities also.
We stayed at Belmar. It's a quieter, smaller property. Since they're the other Buddy Dive location, you get use of the Buddy Dive drive thru on the north side also. I think Buddy sends a boat down a couple days a week also. The dive there is part of the Corporal Meiss site, worth doing for your orientation dive but not the best. We dove it twice.
Five minutes south start all the good southern dive sites, the Hooker, Angel City, Invisibles etc. - they run back-to-back past the Salt Pier down to the Lighthouse.
Dive site descriptions/pictures for a lot of sites on both islands:
Scuba Shore Diving Region: ABC Islands
As mentioned above - if you're considering both on the same trip, fly into Curacao and puddle jump over. It's a lot cheaper, and the local flights midweek are about $60 r/t and it's only 25-30mins. There's also more flights into Curacao than Bonaire. From Phoenix, the only way we can get to Bonaire the same day is the red-eye United flight thru Houston. We were on Curacao by about 2PM thru MIA.
http://www.infobonaire.com/airlineinfo.html Insel Air also has a reasonably priced 2PM departure from MIA if you can get there in time.