Some ideas for making your own superheros:
You could draw your own, coloring as you wish, and scan - if you have a scanner. That's a bit faster than drawing in PSE, or other program.
There are lots of images available on line, some of which are copyright free as well as free downloads; I don't know if superheros are included. Depending on the age of your son, you might find something workable by searching for free coloring pages online, too.
To avoid the girly complaint, use blending or adjustment layers to modify colors, or use papers with a grungy or boy feel to clip to your characters and/or backgrounds.
Good luck with your project!