Having just returned this week........
Pemuteran in North West Bali - http://www.reefseenbali.com/
Labuan Bajo, Flores - http://www.divekomodo.com/
I found everything in Flores at least half the price of Bali, still well set up and very good equipment that was well maintained, less tourists and stunning sites. There are quite a few dive shops in Labuan Bajo but not all are licensed and not all with assess your level of diving capabilities prior. Similarly in Pemuteran, it concerned me that anyone can go on a dive without producing your certificate and get into all sorts of trouble.
I dont think there is a chamber in Labuan Bajo but I could be wrong. It would mean that in the event of an issue, you would need a sea level flight (air ambulance) back to Bali.
Amed (North East Bali), Nusa Lembongan and Nusa Penida are also meant to be gorgeous dive sites. about 8 years ago
Relatively inexpensive and water is clear, but do check the dive equipment carefully yourself... don't just depend on them, not all is certified or up to the standard. about 8 years ago
Here is a nice list of the top 7 dive sites in Bali. I know you asked for all of Indonesia, but it might give you some inspiration
Stefan about 8 years ago
In Indonesia have more dive site.
1. Bali (With Mola Mola)
2. Komodo Dive Center (with Komodo Dragon National Park) Go to http://wickeddiving.com/wd-locations/komodo-dive-center/
3. Bunaken, Celebes, Indonesia
4. Mentawai at Sumatra
5. Rote, East Nusa Tenggara. Nembrala beach.
6. Raja Ampat (one of the best marine park in the world) http://rajaampatdivingresort.com/
7. Alor, East Nusa Tenggara
or you can try Liveaboard, so can know all Dive spot in Indnesia about 4 years ago