You should give a try to Ambon, the feeling of being the only boat around is completely diffrent from Lembeh. Plus if you dive with a company like Dive Into Ambon, you can altrenate every day from pure muck dive into the bay to 25m viz blue water coral dives with incredible bottom topography, some times glass like surface around Haruku.
I think it's a pity to go to Ambon and do not go around the island or enjoy dining in town tasting the Maluku seafood cooking which is probably the best of Indonesia's fooding : smoked tuna, eggplant in almond sauce, etc. This is quite difficult wjhen staying at Maluku divers snce it is so far away from town even though you'll anyway have to rent a driver from DIA as well.
I dived both and more than three diffrent times each location, I would say :
Ambon pros and cons :
- resorts are easy to reach once you're at the airport, Ambon is a hub that is easy to fly to from Jakarta with Garuda (23kgs extra for scuba diving gear).
- I prefer Ambon bottom, more than just black sand, or rubbles, better visibility for muck diving too, it's surprizing that you often get up to 25m at the twilight zone while it lokks really yucky from the surface.
- GREAT coral dives in the south of Ambon.
- Rhinopias, rhinopias, rhinopias... and the Ambon frogfish of course but you really have to be super lucky....
- No boats around, no groups, no loud speaking around,
- Great seafood downtown, also the only place in Indonesia to taste the small GANDARIA fruit, which is simply... one the best fruit you'll ever taste, guaranteed., Halfway between sweet mango and sour starfruit taste, only avaiable february/march..
- Gateway to : 1-Banda isands, most interesting islands in Indonesia for history buffs, 2-Kei Kecil, most beautiful beach in the world 3- Lease islands, one hour ferry ride, Molana with only two bungalows is your private island in the sun you've always dreamt of.
- City is away from the resorts, less accom choice too.
- May be less sites than Lembeh.
Lembeh pros and cons :
- great dive operations, most experienced guides
- More nudibranches, denser life in terms especially of behavior (which comes from the density of critter life)
- easy to couple with other dive spots like Bangka or Bunaken,
- Too many divers, too many people carrying a camera underwater, lots of boats, lots of loud speaking dive groups,- a seleaction of resorts from budget to "too expensive" see below...
- lots of resorts that are too expensive for their actual value, a consequence from the over frequentation,
- Not the feel of really being in Indonesia : you are completely tucked into your resort, unlike Ambon where there is a real indonesian city closeby within a 40mn car ride
My conclusion is that if you only want to spend your time ONLY diving, want to do macro 95%, are a nudibranch buff, don't bother about the landside, tourism, etc then Lembeh is better for you.
On the other hand if you value being the only boat on the site, seeing other people than the group in the resort, want to alternate coral and muck dives, are targeting rhinopias, are ready for a bit of traveling, enjoy good local food, want to spare a few days on white sand beaches then I would recommand Ambon.
Both can be coupled easily with a trip to Raja Ampat.
