I had a good experience diving with Blue Motion Ambon in February 2016.
They are based in Ambon bay. It means the access is super easy from the airport: about half an hour !
Ambon is a paradise for macro diving: rhinopias, frogfish, seahorses, harlequin shrimps, orang utang crabs, ghostpipe fish…
Blue motion is quite cheap: I paid 280,000Rp per dive (9 dives), 200,000 per day for the gear including a torch and 25,000 as local tax.
As a consequence, expect to do a few shore dives but if you stay only 3 days like I did it doesn’t really matter, especially if you go for some night dives.
Quite few options for food a drink near the dive center. Blue motion can book you an accomodation near the dive center if you need.
At the end of the day, the harbor becomes a playground for kids.