I don't remember much from it. It was about a crew that flew around in their ship. The ship got power/ bonus powers from putting different crystals in the engine. I think it's from one of the "mainstream" cartoon channels CN, Disney's various channels, Nickelodeon or maybe Enix
This is Storm Hawks, which aired first in 2007 on YTV in Canada, and then on Cartoon Network in the United States.
Storm Hawks is set on a fictional world called Atmos, a largely mountainous world consisting of scattered, towering, plateau-like land masses known as terras. Directly below the terras lie the Wastelands, the most dangerous area of Atmos, with infernal fires and wicked creatures. Because of the geography, travel is mostly dependent on flight. The technology of Atmos is based around energy-generating crystals, used to power the various devices in the series. Patrolling the skies of Atmos are the Squadrons, groups of warriors who pilot motorcycle-like vehicles called Skimmers that can semi-transform into flying machines. Each Squadron is led by a Sky Knight and these warriors are loosely managed by the Sky Knight Council.
Found by searching for cartoon ship powered by crystals