Luxury liveaboards:
7 Seas : Starting to show her age but the boat and crew are top notch. Top notch dive guide in Tommy but the ratio of guides to divers is low (1 to 6 divers). Can feel crowded if full @ 16 pax! Front 2 cabins aren't the most comfy! (Note I've never stayed in them myself but had feedback from my peeps on various charters)
Damai 1 & 2: Smaller and more luxurious, Damai 2 can be a bit top heavy. Better guide to diver ratio (1:4)
Arenui: Newer boat. Great crew.
Middle/low range:
Grand Komodo: The only Phinisi with a rear "dive deck". Budget but great crew.
Shakti: Only boat that stays in R4 all year around. Shared bathrooms and simple accommodations but Dave knows sites no one else knows about.
In Misool, try the Misool Eco Resort. Sits on the premiere sites on Misool and can reliably dive it till you're blue in the face or purple from exposure!
There are a few resorts now in Norther R4. Raja Ampat Dive Resort just opened 4 mths ago. R4 Dive lodge is run by Grand Komodo. Then there's Kri and Sorido run by Max Ammer, one of the pioneers. However, only at his resorts can you NOT dive on Saturdays due to religious reasons.