Bunaken is about 45 to 60 minutes by boat from Manado.
Most resorts will arrange transfers from the airport for their guests.
Alternatively, a public boat leaves daily except Sundays at 2-3PM from the canal on the north side of Manado market. The cost is Rp 25,000 one way for tourists and Rp 10,000 for locals. It returns to Manado from the jetty in Bunaken village around 8-8:30AM every morning except on Sundays.
You also can charter a private boat to bunaken in the Manado harbor (behind the Celebes Hotel.
