The Bunaken area is perfect for a novice diver, currents are always changing around here and ofcourse you can't be sure if there will be current at a dive site yes or no. By using the tidetable we can estimate the currents and usually this works out very well. There are also divesites around Bunaken which rarely have any current, and if there is a current it's a very easy and gentle current. There are divesites which are famous for it's strong currents but it's easy to stay away from, although at those sites you have the best chances for sharks, barracuda's and other bigger fish.
All and all the currents are very nice here around bunaken.
Diving the mainland around manado provides you with a whole different range of divesites and 90% of them rarely has any current and the diving is awesome, especially if you like macro.
Lembeh strait is also perfect for novice divers conceirning currents, although your buoyancy has to be perfect over there because it's all muck (read : black sand diving) diving over there.
Other places in Indonesia I don't have experience with, I have been working now for 1 1/2 year in the Bunaken area and diving is absolutely amazing...