Just got back from a trip to Bunaken/Lembeh.
At Bunaken, you definitely want to stay on the island not in Manado. Most of the dive sites are situated all around the island - which is at least 45-50 mins by boat from Manado, but just a few minutes from the Bunaken resorts. I stayed at Living Colours which was very nice - beautiful bungalows set in a private garden full of flowers and overlooking the ocean.
At Lembeh - and may I say, this was my first trip to Lembeh, and WOW ! what a fantastic place for diving, I will be returning many times - it doesn't matter so much if you stay on mainland or on Lembeh island since there are dive sites on both sides of the channel and its not so wide.
I stayed at Divers Lodge Lembeh, which was absolutely great - Rob the owner is extremely helpful and nice guy, knowledgeable about the local area and diving - food was brilliant, dive operation very smooth with individual service and no crowds (4 people per boat max with two guides), rooms clean and free laundry !! Only downside is that it is on south part of Lembeh island so a 45 min boat ride up to the main dive sites at the north of the straits. Its a nice 45 mins in the sunshine admiring the big ships that sail in and out of Bitung though.