There are two seasons in the Galápagos: the hot season (December-May) and the dry season. In the hot season, which is also more wet, the surface temperature of the sea is anywhere between 22°C and 28°C. Visibility is better during these months and the sea is relatively calm.
The dry season runs from June to November. The temperature drops to 16-22°C due to the Cromwell Current from the west and the polar Humboldt Current from the south. In this period visibility is less good, but there is more marine life. The clearest water is at the end of this period: October/November.
Whatever season you choose, schools of Sharks and Rays are present year round, including the sea lions, marine iguanas, Equatorial penguins and turtles.
Taking this into account, the best time to go is probably February-March, which is typically the start of the diving season. Note that high season is from November to April and July and August.