We spent a very enjoyable two weeks in Sulawesi splitting our time between Bunaken and KBR. I'd echo the previous comments that it's worth doing both as the nature of the diving at the two places is quite different and makes a good contrast.
We also got to spend a day in the Bangka area and it was possibly our favourite area, the dive in the lagoon was really interesting for critters and you can make your air last a long time when you're at five metres.
At Bunaken we dived with Thalassa Divers and stayed at Hotel Santika which was pretty luxurious (we arranged this and flights throughExplorers and thought is was excellent value for money).
We were impressed with the dive shop, as at KBR the guides were very good and finding and pointing out pygmy seahorses, pipefish, frogfish etc. They were also able to transfer us to KBR by boat diving on the way which was a bonus.
Richard