Robin, my opinion is Indonesia is the best choice of your list, but while it could pass the cost test, it won't pass the time test. Most LOBs in the area do 10-11 days, but oh boy, they are good trips. And it takes a couple days to get there though only one day (on the calendar) to get back.
If you can get the time, Indonesia is fantastic underwater as well as topside for getting your critter/nature fix and people are generally wonderful. Any time left over to spend in Bali would be rewarded as well. While cheaper local boats exist, I'd know Komodo Dancer is a good value. You can fly into Bali and take the boat from there. Right now, I think Komodo Dancer is $3100 and airfare is about $1000. Take out your Pacific critter ID book and what you see in it will be what you see on the trip. All of it.
If time can't be extended, I believe Fiji will be the way to go. The Na'ia is going to be one of the top picks and will visit the best area. People are really fantastic in Fiji too, with my favorite story being villagers waving and yelling hello to us while drove by, while people I see everyday at work won't return a face to face greeting. Na'ia is actually more expensive per day than Indo, and airfare is the same, so your only advantage will be shorter available trips.
Raja Ampat will be out of the question because the trips are all long, it takes another day to get there and probably back because of the times you have to fly out to meet your international flights, and it's another $600-$700 each to fly that additional leg. Having been to both recently, Komodo easily holds its own in that comparison. Go to Komodo during August and September and it's mola mola season.
Last comment is consider PNG. Star Dancer was offering pretty killer rates. However, airfare is typically "killer", literally, as well, but check it out. They also have some specials like buddy weeks, where your buddy is 50% off (?).
Oops, just got this special from Ultimate Dive Travel: Beqa Lagoon (Fiji) 2/13/-2/20 only $1799pp INCLUDING INTERNATIONAL AIR, hotel and diving for a week. Now that is a amazing deal. You could be diving with the big girl resident tiger shark.