Amber
The Archipelago Adventurer II is the more luxurious of the 2. I haven't been on a cruise myself but saw the boat when it was being refitted. I can say they now have great camera tables (Design influenced by Drew
).
The Seahorse is one of the first boats who surveyed the Kaimana/Triton Bay area. Quite a few of the WP staff have been on the boat. Please search the forum for feedback on the boat.
I just returned from the Triton/Kaimana area on another boat, doing a similar route (except I started in Ambon). The area's top dive sites are pretty much current dependent. A few dive sites are not and good for macro. There are plenty of sites along the way to Sorong where there is little current and great macro. Unless you are in control of the intinerary, I'm sure the cruise director will be aware to not have 4 knots currents on every dive. Visibility isn't always the best in Triton/Kaimana area.
Raja Empat has some amazing reef sites which as Todd says is VERY current dependent.
I would say you'd get a slightly better variety of diving doing Kaimana-Sorong but the better diving overall is in Raja due to the proximity of great dive sites. Visibility will definitely be more consistent in Raja Empat. You should have fun on either itinerary.