Ao chegar lá, WikiTravel informa que Bunaken está a cerca de 45 a 60 minutos de barco de Manado.
Most resorts will arrange transfers from the airport for their guests.
Alternatively, a public boat leaves daily except Sundays at 2-3 PM from the canal on the north side of Manado market. The cost is Rp 50,000 one way for tourists (May 2015) and Rp 10,000 for locals. It returns to Manado from the jetty in Bunaken village around 8-8:30 AM every morning except on Sundays.
You also can charter a private boat to bunaken in the Manado harbor (behind the Celebes Hotel).