This is almost an impossible question to answer. It all depends on how much time and budget you have and what type of diving experience you’re looking for. If you want a pristine diving experience, Raja Ampat and North-Sulawesi are maybe the best there is. It is also more remote, so perfect for Liveaboards but for regular dive trips maybe not as convenient. Bali, on the other hand, is a popular tourist destination with lots of facilities and other (non-diving) activities.
TheDivingGuide has (for now) divided Indonesia into the following regions. Check them out to see what fits your needs:
- Komodo Islands
- North Sulawesi
- West Papua (Raja Ampat)
- Gili Islands