When we were there, we did five days in Bunaken, and five in Lembeh. I enjoyed both, but were I to go back, I would spend my time in Lembeh.
Tips for Bunaken: Currents vary, but can be quite strong. Watch for up and downcurrents. Don't discount the shallows at the end of the dive -- for me, they were often the prettiest part, having an unbelievable profusion of fish and gorgeous corals and crinoids.
The walls have dramatic structure and are very colorful, but a lot of the interesting life is well camouflaged and often very small. It's worth staying close to the guide, because they will spot tiny things you will never see. Ours used reef sticks to stabilize themselves, and then we held onto the guides; when they first described this procedure, I thought it was for "lesser" divers, but in the current, it really is hard to be still enough to take a decent picture if you don't do it.
The dive boats hang out during surface interval, and locals with various goods to sell come on board. T-shirts in 2006 ran $5. I was very embarrassed to hear my fellow passengers BARGAINING that price down. I bought a T-shirt and a sarong and the quality of the silk-screening was very good.
I enjoyed Bunaken, but it got very repetitive. I found the scavenger hunt that is Lembeh to be much more fun.