S.B.
I grew up with 3 sisters, and we're all completely different people. My mother was (and still is) excellent at making sure we all understood who we were, and helped us define ourselves. The best advice I can give you is to acknowledge that yes, your daughter is better academically than your son. But there are many things that your son is better at than your daughter. The measure of success is never just one component. To deny that your children are different with different talents is a disservice to both of them. So reassure him that his time to shine will come. Right now, as kids, academics is a major part of their life. But they're going to grow up & have different lives with different goals. Sure, you want him to get good grades for a good shot at a good college, but trust me, a degree from a good school is certainly not a measure of success. It's a measure of how well you can study. If he doesn't already have a hobby that he loves, help him find something to throw his energies into.
Don't deny your daughter's accomplishments, and don't try to pump your son up by telling him he's just as smart. Just let them be different people & help them explore their feelings about that. Good luck!