If you're staying at a resort on Bunaken, you'll need to get to the pier in Manado. The nearest airport is in Manado, about 10 kilometers away from Manado harbor. A taxi from Manado or the airport will run around 100,000 Rupiah. However, most resorts such as Two Fish offer a transfer service from the airport or Manado hotels for little or nothing.
There is a public boat service which leaves the pier in Manado for Bunaken on a daily schedule, but you're much better arranging transport directly with your resort, since most of them are some distance from Bunaken Village, where the public boat docks.