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Raja Ampat
A lot of sea life big things (Mantas, Wobbegong (Bearded) Sharks, Napoleans, Bumphead Parrotfish). You need to do a live aboard to go here. I was on the Pearl of Papua (if that link doesn’t’ work try here). I went in early April and the current was strong (see what the moon is doing before you book) and the visibility wasn’t spectacular (more food in the water = more life but less visibility).
To get to Raja Ampat we flew to Jakarta (CGK)->Makassar (UPG)->Sorong (SOQ). You can use Merpatri Nusantara Airlines or Sriwijaya Air. I ended up using both (different one going than coming).
I paid $2,355 USD for 7 days, a shared twin cabin inclusive of food and diving.
Komodo
Again lots of big things in these waters. Mantas, Reef Sharks, Turtles, Napoleans, lots of Sweetlips, Cuttlefish & Octopus. Had some great diving here on my 6 day Liveaboard with Dive Komodo. The dive outfit was great. At $175 a day (inclusive of lodging, dives, equipment and food) + 15 a day for Komodo park pass they are on the budget side. But the boat was comfortable enough, the food and crew were excellent. In Komodo you can do day trips or 3, 4, 5, 6+ day liveaboards. Dive Komodo offered us 3 or 6 day but we know some people that did a 4 day. Just ask them because they have day boats that go out all the time so we had people getting on/off the liveaboard on various days. We had two DM’s, Fabi and Wai. Fabi was good and Wai was fantastic.