I think I gave you my advice on another forum.
Just some other stuff I can add on Ambon :
- don't count on the Psychedelic frogfish, nobody's seen it since early 2011.
- If you want additional luggage weight with no business class cost better take Garuda flights which accept up to 35kgs for divers (even though Garuda's raised their domestic flight prices this year). Just specify "Menyalam, boleh tiga puluh lima kilo" pointing at your dive bag
As for the cleanliness of water, it depends on the tides : rising tide Ambon bay is quite clean with sometimes vizibility that Lembeh would never expect. I 've already had 25-30m in Laha. But don't ever dive a strong flowing ebb tide you'll get all the disgusting stuff from the bottom of the bay.
If you've never been to both and you're starting with photography I'd suggest Lembeh at first hand. Easier, denser in terms of critters, Ambon is more of a specialist spot. As for the environment, and except if you stay in your hotel or at Maluku Divers it will be more difficult for you to get understood downtown than in Northern Sulawesi. Be prepared for a little bahasa.
Out of scope : Drew you have to give me your hints on oleh-oleniah hunt from the outer islands in Ambon. Never found anything interesting, I reckon Bandanaira is a much interesting place for that (at least for edible stuff).