Raja Empat is just not a budget / backpackers location. Only choices are of 3 resorts (2 in the same proximity run by Max
Main page and a new one opened up in Missool (south) run by Andy
Misool Eco Resort - About and then the live-aboards besides the big boys the smaller Grand Komodo boats are there on occasion (these can be a little cheaper (more rustic accommodation and meals...depends on what you are looking for). Back in the good ole days there were only 6 or so running but however Raja's popularity has grown quite abit with a lot of new operators trying to cash in on the market. I would stay with those that know the area / dive-sites to ensure value for money and disspointment. IMHO the best diving is down in Missool - far better than the northern sites (best up north Melissas Garden, lohloh (button Is) Eagle rock (when possible) Cape Kri And Sardine Reef), Down south too many to mention