The stealth ship had a devastating close range rail gun. Rail guns use powerful electromagnets to accelerate projectiles to very high velocities in fractions of a second. In 2010 the US Navy built a rail gun that fired a 7 pound round at 10 times the speed of sound (7,600 miles per hour). Provided you have a good enough source of electricity, you could launch projectiles at relativistic speeds (close to the speed of light).
The transport ship, 'Guy Molinari', was named after the Staten Island Ferry that the author, Daniel Abraham, used to take to work.