I've done this before. The easiest method is to simulate the projectile, record points along its trajectory and note the closest point to the target. What I then do is get the target's location + (target velocity * time taken to reach closest point*) to get the location it would be by the time the projectile reached it. All you need to do then is Math.atan2 the new coordinate with your ship's coordinate to get the angle you need to be at to hit it (or you could draw a marker on the HUD at the new location if you prefer).
For my purposes, this is efficient enough, and can deal with multiple targets at once without any performance hits. If you want it to be more efficient, simply multiply the projectile's velocity and put less points along its trajectory.
*note that the time taken to reach the closest point is that point's index in the array.