It depends especially on the level of comfort and facilities on board you are looking for:
You can visit the Galapagos any time of the year as there is always something wonderful happening in the Islands, especially with wildlife’s behavior and natural events.
From mid-June to early-December you have a mixture of warm and rain (afternoon showers), and Ocean waters are warmer and calmer due to the “El Niño” current. From mid-December to early-June is the cool/dry season on land and Ocean, especially because of the passing of the “Humboldt” current through the Archipelago.