There is a good range of hotels, resorts and other accommodation options on Bonaire. Almost all of them are along the sea fron of Kralendijk stretching north of the airport, and many cater to divers.
The grand-daddy of all the dive resorts is Captain Don's Habitat. The late Captain Don mapped out many of the dive sites and was instrumental in the drive to establish the marine park which protects the reef. The resort has its own dive shop and boats, and the house reef itself is one of the best dive sites in Bonaire. When I stayed here in 2014, I dived the ‘La Machaca” almost every day, and almost always found something new, such as frogfish, seahorses, juvenile moray eels, and more.
Right next door to Captain Don's is Buddy Dive, which caters more to people who would like to explore the dive sites of the main island on their own. You can rent a pickup truck from the resort and drive yourself to any of the 60 or so identified dive sites around the island. When you've emptied your tanks, the resort has a drive-in refill center where you can get more air and be on your way quickly.
If you need a larger accommodation with two or three bedrooms, or would like some self catering options, then check out Sand Dollar Condominium.
At or near the top end of what's on offer are the designer villas of Piet Boon Bonaire:
Set along the waterfront in Kralendijk, the island’s tiny capital, Piet Boon Bonaire is a collection of nine individually styled villas. Six of these are right on the beachfront, with ultra-spacious and expertly crafted living spaces leading out onto private terraces, which have cool pools and easy access to the sea. Three additional villas sit further back from the shore but just like the beachfront properties, they are unmistakably the work of Dutch design icon Piet Boon, who has a reputation for designing bespoke, luxurious beach villas worldwide.
You can find more options for hotels on Bonaire and compare rates from several web sites at Hotels Combined.