Gajah, I would recommend you give Bali another chance. Especially given your lack of time. Consider flying directly to Bali, do your diving then head to CGK.
I've been to Weda in Halmahera and to Walea in the Togians. Plan on a full day to get there from GGK for either. As Luko and Gun mentioned, there is diving on Ternate, I saw some shore divers exiting the water when I was driving through the town on the way to Weda. But the operators may be difficult to find.
In Raja Ampat, another land resort to consider in Raja Ampat Dive Lodge.
In Ambon I dived with Dive Into Ambon and can recommend them, as well as the diving in Ambon. But same as Lembeh, the waters are full of trash, not a big deal.
Gorontalo diving is okay, the operator, Miguel's Diving was good in 2012. Probably still good if the manager Rantje is still there.
I guess you have to decide: How much do you want to dive in a new place vs getting an extra day or two of diving in a place easier to get to?!
In my opinion, your best choices are either Bali or Ambon. I've dived 4-5 times in Bali, only once in Ambon, so I may go for Ambon for myself, but if you haven't had a good diving trip in Bali, I recommend that for you, simply because you can fly in there directly and have several flights a day to CGK when you are done. I don't know how many daily flights between Ambon and CGK.
I'll echo what others have said, Bali diving is Good!
Hope this helps.
ps: When you say, "It's easy to fly into Ternate" from CGK, I'll note that I got delayed for hours transiting through Manado on my way to Ternate from CGK.