I'm assuming that you're concerned about Malaria. So I'll start with a disclaimer: I have no medical background and no claimed expertise about mosquito habits.
That said, I don't think that you need to be overly concerned. Since you're going on a liveaboard, I doubt you'll have any trouble.
When I was there (Shakti, December '08) I had no problems with mosquitoes at all.
I don't think mosquitoes venture out to sea (not even shallow anchorage areas). I don't know if it is the breeze or cooler air over the water that keeps them away, but I've never seen any on the boat.
You might run into mosquitoes in the Sorong Airport or if you spend any time on land. Just make sure to cover your exposed skin with repellent during those limited exposure times.
I was always told that malaria carrying mosquitoes are only active from dawn to dask - a time when you are most likely to be on board your boat. (Dengue fever carrying mosquitoes bite during the day - but they are more common in urban area than in rural areas)
I hope this helps.