Combine the lime juice, olive oil, chili powder, garlic and onion powders, 1 teaspoon salt, and ½ teaspoon pepper in a large food storage bag. Add the chicken thighs and make sure the marinade coats the chicken completely. Let marinate either at room temperature for 20 minutes or in the refrigerator for up to 4 hours. If refrigerated, let come to room temperature before cooking.
When ready to cook, preheat the oven to 400 degrees. Place a wire rack on a baking sheet and spray the rack with gluten free nonstick cooking spray.
Grind the tortilla chips into fine crumbs in a food processor or by putting in a food storage bag and rolling with a rolling pin. Place in a shallow bowl. Beat the egg with a teaspoon of water in another shallow bowl. Put the flour in another bowl and season with a pinch of salt and pepper.
Dredge each thigh first into the flour, then the egg, and finally in the tortilla chips, making sure to coat well and press the tortilla chips firmly onto the chicken. Place on the wire rack, spray with cooking spray, and bake for 45 minutes or until they reach an internal temperature of 165 degrees.