Airlines that fly to the Galapagos include Tame and Aerogal (or Aerolineas Galapagos). Both offer flights to San Cristobal and Baltra, which are the two main travel hubs in the Galapagos. Ticket prices are very similar with both, though if you fly from Guayaquil, the cost is cheaper than if you fly from Quito. Flights in the low season (normally May to mid June and mid September to the end of October) are usually cheaper. Note that almost all flights from Quito to the Galapagos Islands will touch down in Guayaquil en route. Student discounts are often offered for those with an ISIC card.
It is best to book the flights in conjunction with your cruise or hotel. Our advice would be to let an agent / hotel / cruise operator book the flights for you. The price will be only marginally more expensive if at all, and your trip will be far less complicated. If you do choose to book the flights to the Galapagos yourself, it is important that you reconfirm them 24 hours before departure otherwise you might get bumped off. And make sure you book a flight to the correct island!
Note that it is almost impossible to travel by boat to the Galapagos Islands. Apart from practical difficulties, it would take about a week to get there, so you must fly. See the section on Ecuador flights for route maps and more information.