Since I had posted here earlier looking for recommendations and advice, I thought I should follow-up with my own trip report for others who might follow. I'm not sure if this is the best location for a trip report, but I'm sure the forum moderator can move it if necessary.
My wife and I recently spent a week on each of Rarotonga from July 8-15, and Aitutaki on July 15-22 2012, doing four dives on each atoll. We decided to stop in the Cook Islands as a free stop-over with Air New Zealand while moving temporarily (10-12 months) to New Zealand from Canada. We are both advanced open water divers with 120+ dives from 10+ countries, mostly around the Caribbean.
On Rarotonga we dove with Pacific Divers in their aluminum boat with 3-5 other divers of various levels going out from Avarua Harbour on the North Side. There were a number of dive operators, we picked the ones closest to where we were staying in Muri Beach at Aito Apartments (which we loved). My impression was that there were very few fish, and very little healthy coral. There were a few small schools of smaller fish, and a lot of flat yellowish "mushroom" coral. We did see white-tip reef sharks on 3 out of 4 dives, two turtles, a couple of small eels, and a napolean wrasse. The visibility was fairly good at 40-90 ft. The topography varied between flat ridges and shallow ravines leading down with plateaus with edges that dropped off to thousands of feet. There At 23C/73F with an air temp between 16-20C we found the water to be a bit chilly for our 2/3mm full suits. My wife and I each purchased a 1mm rash shirt to help compensate. The staff at Pacific Divers were competent and engaging; they lead dives very well, always left one person on boat with oxygen. Because we found the diving expensive and only so-so, we opted to do other island activities; hike the cross-island track, kayak around Muri lagoon, snorkel in the marine reserver near the Fruits of Rarotonga, and walk-tour around Avarua and Muri Beach. Make sure you try the island beer from Matutu Brewery and the pizza from Trader Jacks.
On Aitutaki we dove with Aitutaki Scuba, going out in a small boat with a local dive master and boat driver. There was another diver operator "Bubbles Below", but we had a recommendation from someone on Rarotonga to dive with Aitutaki as they only take experienced divers out. (Yes, my wife and I can be newbie snobs sometimes, we love all divers but prefer to go out with more experienced divers when we get the chance.) Underwater was very similar to Rarotonga, a general lacking of fish and healthy coral. However, there were large napolean wrasse everywhere! I think we saw at least 2 different giants on each of the four dives. We also saw white-tip reef sharks, some large green turtles, a school of 3-4 eagle rays, a couple of fast-moving 2 ft. yellow-fin tuna, several large barracuda as well as as large school of juvenile barracudas, a stonefish or two, and a couple of small green moray eels. The topography was stunning, with big steep ravines and walls, the occasional sand-filled plateau, and everything was covered in mushroom coral. The visibility was amazing on most dives, I'm sure we had well over a 100 ft most times, minus the occasional sand storm draining off the lagoon. Being ~2 degrees closer to the equator, the weather was a bit warmer at ~26C/79F. On two of the dives we clearly heard whales calling; later that day we talked with some folks who said they watched a pod of humpback whales breaching and blowing a little further around the island from where we would have been diving at approximately the same time. Very cool! (I had heard of divers seeing them up close from both Rarotonga and Aitutaki between July and September each year, there was even a video from someone's dive trip showing the whales up close, it's somewhere online that I can't find anymore.) The dive operation and staff was very professional, courteous, and engaging. Our boat captain and divemaster "Dawn" brought fresh tuna sandwiches and cracked coconuts for us between dives. Anyway, my wife and I still found the diving expensive (very remote islands) and only "so-so" as compared to our other dive experiences so we opted to do other island activities such as snorkel, lagoon tours, kayak, rent motor-scooters, watch local rugby, and drink beer. The lagoon tours are a must - make sure you snorkel at least once out in the lagoon near the clam farm. There is also good snorkelling on the west side near Etu Moana Resort, or around the private motu Akitua at the east end of the airport runway. Be sure to visit one-foot island. For a good beer visit the Boat Shed, good coffee and prepared lunches can be found at Koru's Cafe.
My wife and I really liked Rarotonga and Aititaki. It's very safe, we've travelled to Honduras, Jamaica, Mexico... The people are extremely kind, friendly, and laid-back. The main language is English. The islands are visually stunning, while each are different and interesting in their own ways. I'm very glad I got to see and experience some of the Cook Islands. All that said, I probably won't ever go back. I like to dive too much and I would rather pay the extra money to go somewhere new with better diving; perhaps Fiji, Tahiti, Palua, Samoa, Indonesia, Malaysia, etc.
If anyone wants more specific advice on Rarotonga or Aitutaki, post a response here and I'll try to help.