Flights to the main Galápagos airports in San Cristobal and Baltra depart from Quito and stop en-route in Guayaquil. The Quito-Guayaquil flight lasts about 40 minutes, and the Guayaquil-Galapagos flight takes two hours. Since the archipelago is one hour behind mainland Ecuador, passengers leaving Quito in the morning will land before noon. For a significant portion of the flight, passengers travel over international waters, so they can make use of duty-free shopping.
Two airlines, TAME and Aerogal, service the Galápagos Islands. Children and infants do receive a discount. According to TAME, the low tourist season is from May 1 to June 14 and from September 15 to October 31. Times vary and change in different seasons, but the prices are fixed, so there's no need to comparison shop.
If you book a cruise, the travel agency generally arranges your flight for you. Even though there is usually some availability on flights to the Galápagos, it is a good idea to make independent flight reservations at least a few days in advance. Travel agencies will block seats for their all-inclusive tours, but then release them on the day of the flight if there are cancellations or unsold tour spaces. So if you are desperate to get to (or return from) the Enchanted Islands, you should be able to find spaces last-minute, especially during low-season.
Since flight prices are fixed, you can change the date of your ticket after purchasing it without penalty. This policy can come in handy if you—like many other tourists—get caught up in the small-town charm of Puerto Ayora and decide to extend your stay: just stop by the TAME office on Charles Darwin Avenue anytime before your flight to make alternative arrangements.
Furthermore, if you decide after sun-bathing for a week that you want to spend more time in coastal climes, you can easily change your final destination to Guayaquil. This requires simply checking your luggage to Guayaquil; no ticket change is needed.
It is not feasible to take a boat from mainland Ecuador to the Galapagos: it is a three-day trip over rough waters and there are currently no ships or agencies selling this service.