I've never been to Kri Eco but i have recently stayed at Raja Ampat Dive Lodge (December 2011 spent Xmas there) I was right at the RA Dive Lodge jetty when the Mandarin Siren sank. Could literally see the smoke etc .
My whole family went and that meant extended family as well (about 20-25 of us in total including kids). We basically booked nearly the entire capacity but only about 10 people dove and we took our Open Water Cert there. I can't say much about the dive guides cause we never used their local dive guides etc cause we brought our own dive instructors but while i was there, i did get a chance to get to know them. They're all friendly local guys. Most of them are either from Sorong or other parts of Indonesia. I'm guessin the fact that I am Indonesian also helped with the communication.
The service of Raja Ampat Dive Lodge was very good overall. Since we brought our whole extended family etc, some of the aunts etc wanted to cook and they let us use their kitchen etc and even to create a make shift kitchen at the front of the dining area where the older women of my family could cook etc. They were definitely pretty accommodating but like i mentioned, it may be partly cause we were Indonesians as well. Food by the local chefs was not bad. During our time there, it was buffet style but from what i heard, when there is not as many visitors, it'll be *order* style. Coffee and tea etc was always available.
There was wifi in the dining area though it was pretty slow but they may have changed it. You can also bring your mobile phones along cause there is reception for Indo telephone companies. I'm not sure if Kri Eco has reception.
I particularly enjoyed the stay at the Dive Lodge partly due to the jetty. The amount of stuff you see right under the jetty is amazing. Our dive instructors went for a night dive and shot some photos of a pair of mandarin fish mating. The mangroves around the dive lodge also provide some interesting find. During our stay there, we saw 2 walking bamboo sharks just at the beach front where all the mangrove trees were.
Would definitely recommend RA Dive Lodge but like i mentioned, i have never gone to other RA resorts so i am not sure how the dive lodge compares. One thing for sure is that we've booked our rooms for RA Dive Lodge this coming December again except now, we're goin as AOW holders!
just realised all my writing so far was not answering OP's question. In terms of best local dive sites, i think they're pretty near each other cause you'll have to go by boats anyway but the Manta Spot and Blue Magic spot was not very far from RA Dive Lodge. Im not sure about the surcharge thing but if i remember correctly, it was free for us maybe due to the number of ppl. We practically took up 3 ferries to get the whole family and luggages there.
What ever your choice is, i am pretty sure you'll have a good time at Raja Ampat.