I use Shake, but it's overkill for a simple muzzle flash. I agree that the best thing to do would be to grab a paint program and paint what resembles the muzzle flash of your gun (you can check some of your favorite action movies for reference). Then bring it into Final Cut Express or Final Cut Pro and use one of the blend modes to overlay the flash. I think the blend mode "Screen" would work pretty well.
P-Worm