"My wife and I dove Galapagos this past summer aboard the Aggressor. Now we are thinking about diving Cocos Island. Has anyone been there w/ Aggressor? I wouldn't think of using anyone else as we have had terrific experiences with them both in the Galapagos and the Turks and Caicos."
The relative merits of the Aggressor (and Peter Hughes for that matter) vary by location. These are franchises, but must maintain certain Aggressor standards. The Galapagos Aggressors are the cream of the crop. I wouldn't consider any other live-aboard in the Galapagos.
Conversely, I wouldn't choose the Palau Aggressor because there is a better choice in Palau.
The Okeanos Aggressor has a good reputation, but the reputation of the Undersea Hunter and Sea Hunter are even better and would be my first choice.
" The biggest objection that my wife had was the initial run from Costa Rica out to the island, but after having done a 22 hr run from Darwin to the main islands of the Galapagos it looks like that is no longer an objection."
The Cocos crossing can be rougher than the Darwin/Wolf trek, but you never know. Because it does take longer to get there and there isn't any diving along the way, make sure you book a longer trip.
"I know that there are plenty of hammerheads, but what about Whale Sharks? Sure would like to see some more of those guys! We swam with 17 this summer. I know very little about it and would like to learn more."
You were quite lucky. Cocos WS sightings are not quite as dependable. Inquire about the seasonality of WS sightings. They may be seasonal, just like the Galapagos (July-Oct).
Hammerhead sightings are also hit and miss. El Nino caused the hammers in the Cocos to deeper water. They are there, but sometimes much deeper. The Cocos can be more dependable for seeing other pelagics, e.g. rays, white tips, silkies, etc. along with baitballs.
You can ask a group of people who have been to both and they will split as to which is better, simply because the experience in each can vary significantly. If I had the time to do the 10-day trip, I would do the Cocos. If I really had the time and money, I'd do the Cocos/Malpelo trip. If I wanted Whale Sharks for almost sure, I'd go back to the Galapagos during the season.