Hello vaapa, I've not been to that part of Indonesia, furthest South I've been was Alor, furthest East was Seram. But, a quick look at a map of the Aarafura Sea, shows it to be very shallow compared to many other parts of Indonesia. In my experience, this usually means poor diving due to the relative lack of nutrients that would come from having colder, deeper water near dive sites. Those nutrients that come up from the deep in currents and upwellings are a large part of what fuels the food chain and provides for more species diversity and bio-mass. Alor, which is some of the best diving I've ever done, is constantly subject to cold water upwellings, which sometimes brings up water from the deep which is as cold as the high 50's F. This is not coincident to the great visibility, diversity and great amounts of flora and fauna found in and around Alor.
The visibility in the coastal areas of South Irian Jaya will probably be very low, given how many rivers empty into the Arafura Sea. Large parts of the Asmat region are swampland, which in some places goes over 100 miles inland. Sounds like mosquito and crocodile heaven. If there's any good diving in the Arafura, my guess is that it will be very far offshore and known only by fishermen... -Andy