Hi Seeker646, I run a dive travel agency based in Makassar, let me answer some of your questions.
Best time - Sailing and diving is possible all year round in Indonesia, there are two distinct seasons, November to March in Raja Ampat, May to September in Komodo, this is due to the winds changing direction from East to West and vice versa. In October and April, most boats transit between these two areas, usually going through the Banda Sea, or North Sulawesi/Wakatobi.
So October to April, where the sea is still expected to be steady and calm is the season. It is important to note that a liveaboard is discouraged from May to September because strong, heavy winds and rains are more likely to occur.
Land v Sea - Raja is a huge area, so it very much depends which liveaboard you go on, some are only 7-8 nights so will do either the North or the South, the North is well served by resorts, and you will probably get to many of the same sites from a resort as you will from a boat, but there is really only the one resort in the South, the very nice and quiet expensive Misool Eco Resort. But if you take one of the longer, 12-14 night trips on a boat you will get to see both North and south and everything in between, and a number of boats have their own "secret" sites they have found en route, which is where the boats do have the advantage. Most resorts have a 7 or 14 night package and only do transfers on set days.
Logistic - its pretty easy, there are daily flights from Jakarta to Sorong, which is where you have to start any Raja trip, land or boat based, Garuda is the most reliable and has the most generous luggage allowance for divers, allowed 20kg/pax overweight IDR 23.000/kg (Plus as long as the dive gear is packed separately another 23kg/person for dive gear/sports equipment and 7 kg hand luggage allowance) but it's not a direct flight so Express Air is the 2nd alternative.
The boat or resort usually picks you up from the airport and from there to the harbour.
Extra costs - park fees just gone up to 1,000,000 rupiah this is a year long tag, which is odd, since few people travel back in the same year, but that is Indonesia for you! Visa on Arrival again just gone up to US$35 for 30 days, as above any excess baggage, some of the resorts charge for transfers above and beyond the package, eg Misool, €300 per person. then depending on which boat, nitrox, equipment and fuel surcharges are also applied.
The 2015-2016 season is already quite booked up, especially over Christmas but there are still some available cabins.
If you have any more questions, you can reply here or email me at
info@diveoptions.com.
Hope that helps.
Cheers
Jonathan