Ben and Adam use this as slang for masturbation. Probably specifically male masturbation. Because it reminds them of the hand motion, I guess? What do their penises look like?
Anyway. In one episode Ben Sisko abruptly gets a new inappropriate hobby just in time for the war with the Dominion. He builds a hand-cranked
sailboat starship using ancient Bajoran plans. Jake accompanies him on the maidenhead launch.
To get the ship's solar sails to work they need to manually turn cranks, presumably those winch the sails in and out.
So basically, the Sisko boys had some alone time in a sailboat and spent most of it crankin' it.
Oh! I just remembered. In the beginning of the episode Ben Sisko barges in on Jake, something you should never do to a teenager because maybe he's crankin' it. But that's OK because Ben invited Jake to come crank it with him on the boat.
Note: The term "Jake"ing Shuttlecraft refers to Jake Kurland committing grand theft previa.