Sangalaki area is one of my favorites for the diversity of diving experiences. I stayed in Derawan a few years ago, and a pretty nice bonus there was waking up to find turtles grazing on leaves outside your water-bungalow window. On my secind trip to the area, we stayed at Maratua paradise, which I think is slightly better to live in. The house reef is splendid. The resident thresher shark didn't show up during our stay (this is why we chose Maratua), but we nevertheless enjoyed loads to time with grazing bumpheads, an occasional eagle ray floating past.
It's easy to make day trips to Sangalaki -- which has fantastic dives. Or, as Drew suggested, you can split your stay with some time in a resort on Sangalaki (Nabucco looks nice, I think we had lunch there on a day trip once).
By the way, I am not sure of the science on this, but maybe you can find out if more Manatas prefer to show up during some phase of the moon or another.. if your dates are flexible, it couldn't hurt to try and improve your chances.
Our trip reports and photos are linked from here: