It's cheaper to fly from Guayaquil than Quito (the plane leaves from Quito and stops at Guayaquil, anyway). There is only one airline and the price is fixed for tourists at a level depending on whether you visit in high or low season. Take lots of cash and negotiate a cruise when you get there - mainland agencies simply do not know which boats have space, and are much more expensive. South American Explorers in Quito has hundreds of trip reports to help you get a shortlist of cruises. A small boat with around 12-20 passengers is best. Don't go on a huge boat or a luxury cruise because it won't be as much fun. Make sure you get good snorkeling gear & an underwater camera because the snorkelling is even better than the diving, and free!