It depends especially on the level of comfort and facilities on board you are looking for:
Taking a Galapagos cruise is considered the best way to explorer the Galapagos as it gives you the opportunity to reach the remotest islands as you sail at night from site to site, which means more time to enjoy the location and day’s activities.
However, if you are susceptible to sea sickness the feasible alternative is taking a nice land-based tour with hotel accommodation on the populated Islands of Santa Cruz, San Cristobal and/or Isabela; from here you can enjoy interesting day-tours to the nearby sites or Islands; you will also have the possibility to enjoy snorkeling and other activities while taking day-tours.
First, you must get to Ecuador Mainland. Make sure you arrive to Quito or Guayaquil at least one day before your departure to the Galapagos; there are no direct connections with international flights and flights to Galapagos Islands depart from mainland Ecuador early in the morning from Quito and/or Guayaquil.
Visitors arrive by plane from Mainland (flight takes about 2 ½ hours) with three main Airlines: AVIANCA, LAN and TAME and arrive to Galapagos to one of its two Airports: One in Baltra Island and one in San Cristobal.