I was just in Raja-Misool-Kri-etc in December 2009....most definitely take the liveaboard route. This area is too massive to only experience a small portion of it. I had the opportunity to look at several of the R4 eco-resorts which all seemed very nice, but I am very happy I dove from a liveaboard and thus was able to experience many more areas of West Papua.
Thanks for the advice. Any recommendations on liveaboards would be appreciated!