It depends especially on the level of comfort and facilities on board you are looking for:
Although the Galapagos Islands are located in the Equator, but it has moderate, drier climate rather than typical tropical weather. This because of three confluent Ocean currents that determine the two yearly seasons in the Archipelago: cool/dry season from mid-June to early-December and the wet season from mid-December to early-June.
Average temperature range: 69°-84°F / 21°-30°C. Weather in Galapagos has variations on each season.
If you are taking a Galapagos Cruise or package, it is best if you book your domestic flights to/from Galapagos from Quito, Guayaquil or mixed route along with your cruise. This because cruises/tours must follow a pre-approved itinerary by the National Park’s Authorities, and all start their itinerary with specific arriving flights to the Islands, and cannot wait for stragglers arriving on different flights other than the one used by the rest of the group.
Catching a cruise when arriving on different flights that are delayed or arrive on different timings can be very expensive and in some cases, impossible, causing distress and unwanted non-refundable trip cancelations.
For this reason, all operators recommend booking your domestic flights along with your cruise or tour to align with the operation and avoid any issues. Get full details on logistics and traveling to the Galapagos.