Tripoint (Merchanter #3) by C. J. Cherryh

Merchanter Cargo Chief Marie Hawkins has never forgiven the crime, nor sought justice. Only vengeance. And, for 23 years, the Hawkins's clan ship, Sprite, has lived with her vendetta - and with her son, Tom, the boy sired in the violent assault.

Marie's attacker, Austin Bowe, is captain of the Corinthian. When both ships dock at Mariner Station, Marie vanishes and Tom searches for his mother...only to find himself trapped on Austin's ship with a half-brother he never knew he had and a crew fanatically loyal to Bowe. Now as the Corinthian flees the pursuing Sprite and a raider guns after both, the lives on board the two Merchanter ships are in the hands of Tom Hawkins. To save them all, Tom must trust his sworn enemy...

His father.