By all accounts, the diving around Raja Ampat is about as good as it gets, with an unmatched diversity of marine life, in a wide variety of environments ranging from walls, to slopes, to clear mangrove swamps. While the area is still "the back of beyond" at the furthest edges of Indonesia, there are still a growing number of live-aboard options available, as well as some very attractive looking dive resorts.
Most of the live-aboard boats leave from and return to Sorong in Papua. Flights to Sorong are available from Makassar and Manado. The resorts in the area will generally provide a transfer service for you from Sorong. Many of the operators can also help you with domestic travel arrangements, which can be rather tricky in Indonesia.