The best idea is to ask your accommodation and follow their guidance. Or simply ask them to arrange this transfer for you.
It turns out the resort charges a lot for a private transfer. No surprise there.
about 600 000 R. get taxi from airport (fixed price) to harbour where the speed boats leave for Bunaken. there are a number of boat captains keen for work.
I ended up organising it from my resort. It was certainly easy to organise in advance but I would say it was not cheap. I suspect you might be able go to Manado pier and do it yourself and save some money.
Thanks flyingalot. Will try and look for public boats.