December is a great time.
At Dive into Ambon your can dive both the traditional muck sites in Ambon Bay, and the sites out of Ambon Bay. We find a lot of critters out of Ambon Bay that aren't found in it.
We dived with Dive into Ambon in December 2014/January 2015 and they run an excellent operation. I can confirm that December is great time to dive there and that there a lot of critters found outside dive Ambon Bay that cannot be found inside it.