I have done a Liveaboard in the Galapagos and Cocos both with the Aggressor.
Galapagos:
I visited the Galapagos in January, the temperature averaged around 20 degrees. Most people were in either 7mm wetsuits or semi-dry suits. Wolf and Darwin were outstanding, we had schools of up to 300 hammerheads up close on a couple of the dives. We also had a school of Mobula rays (the dive guide said he had never seen anything like that... 500+) We had a few Mantas and Eagle Rays as well as Galapagos shark. We may have been lucky as I spoke to somebody who also went to the Galapagos and they saw nothing.
There was lots of surge and current. The other diving was mostly average other then a couple of stand out dives with the marine iguanas and sea lions. The Red Lipped Bat fish were also very cool. I would say 50% of the diving was the best i have ever done and 50% was forgettable.
I wasn't very impressed with the Aggressor, the organisation wasn't great and they didn't have all the equipment (wetsuits/ torches/cameras) that the guests had requested. We also lost a dive at Wolf which could have been avoided.. very annoying. I've heard better things about the Hunter.
I think there are restrictions on how many dives you can have at Wolf & Darwin but try and find a Liveaboard who offer the most dives at these places. There are some interesting islands you can visit before or after to see the wildlife.
Cocos:
The beauty about Cocos was the temperature was around 28 degrees for the whole trip (September) The crossing is long and can be quite rough but we didn't have it too bad. The diving was quite similar to Wolf & Darwin with the hammerhead schools but not quite as close up and not quite as many. We saw hammerheads on most dives and we also saw a couple of Whale sharks.. also dolphins. There was something quite special about Cocos island, I would love to go back as we were told we didn't see it at it's best. There were divers on board who did the trip every year and they said they had seen schools of 300+ hammerheads along with lots of Whalesharks & Orca's!
The Aggressor was good, the staff were great. Rooms a little dated but its a boat built for the crossing! Again, heard good things about Hunter.
We also visited Monteverde, Manuel Antonio and Arenal which were all excellent.
I don't think you can go wrong with either of these places, I loved both places and would do both trips again in an instant but I think I preferred cocos because you were not restricted to the hammerhead dives and also the temperature was much better then the Galapagos.
Be careful with El Nino if you are booking this trip soon... do some research to see what effects this has had.
I would love to visit Malpelo and Socorro so looking forward to see some reviews on these places!!