This debate could be argued quite soundly and passionately in either direction til kingdom come - like dogs vs. cats, motorboats vs. sailboats, Force fins vs. split fins vs. paddle fins.
About the only thing that all might agree on is that both are world class destinations that should be dived as many times as possible before sharks and other big animals are rendered extinct. You will not be disappointed going to either one - unless you happen to have a really unlucky trip.
If I were you, I would think about my top two or three most critical requirements (whatever they may be: number and size of whalesharks, price, diversity, variety and qty of pelagics, water temp, length of boat ride, land visits, etc.) and see which destination is better able to meet those requirements.
With that said, for the timeframe of October/November that you specified, for me it would definitely be Galapagos. Altho Cocos can be dived yearround, the best Cocos months, with the best chance of seeing whalesharks, are - in my opinion - June thru September.
Comments on your comments:
- I've never dived Galapagos with less than 5mm (7mm was better) - I've gone in May, twice in October and once in November. In the Northern Islands, I've typically seen mid-70s, mid to hi 60s in the Central and Southern Islands, and as low as lo 50s in the Western Islands. In Cocos, I've never had to use more than 3mm - I've gone three times in July and once in September. When I've run into a themocline in Cocos, it's usually been lo 70s, but of course, when you go from 80 to lo 70's, 72 feels more like 50.
- I haven't done any of these Aggressor boats but do have favorable impression of either of the Galapagos Aggressor boats. I'd love to get on one of their longer-than-7 day trips. They seem to be the only boats offering longer trips. In Cocos, even tho I'm sure that Okeanos is a good operation, I've only done Undersea and Sea Hunter - they may be pricier, but if you've read past threads, you will know that lesser number of passengers and much better tenders make the latter a better choice for many.
Air: American, Continental, Delta and US Air all fly into San Jose, Costa Rica. It looks to me like you could do the trip with just one change of planes. American and Continental fly into Quito and Guayaquil, Ecuador, so those could conceivably be single change of plane trips as well. I don't know who else flies there.
Sounds like you've got a busy diving year coming up - PNG and Eastern Pacific - not to mention presumably yearround diving in Hawaii. Congrats.