On the island you have the choice amongst a number of homestays, with rates starting at around Rp. 50 000 per day and person incl. fullboard. If you only go for the cheapest option don't complain afterwards if the water in your mandi (bathroom) doesn't get filled up regularly, or food isn't quite as nice as you had hoped for. Life in North Sulawesi in general isn't as cheap as in other regions of Indonesia, and most things on Bunaken have to be brought in from Manado. Depending on the season even fish can be pretty expensive. Better think twice before you try to bargain down prices which are already cheap; for the locals it could mean the difference between being able to eat 3 or only 2 meals a day, or buying school books for the children or not.
Some of the dive operations on Bunaken are offering more upmarket accommodation with running water ((Living Colours) and even hot showers (Cha Cha Nature Resort).