In a large bowl, whisk together lime juice, honey, soy sauce, olive oil, minced garlic, cumin, black pepper, and red pepper flakes (if using) until well combined.
Add the chicken thighs to the marinade, ensuring they are fully coated. Cover and refrigerate for at least 1 hour, or up to 4 hours for more flavor.
Preheat your grill or oven to 400°F (200°C). If using a grill, lightly oil the grates.
Remove the chicken from the marinade, reserving the marinade for later.
Grill the chicken thighs skin-side down for about 6-8 minutes, then flip and grill for another 6-8 minutes until the internal temperature reaches 165°F (75°C). If baking, place the chicken on a baking sheet and bake for 35-40 minutes, basting with the reserved marinade halfway through.
Once cooked, remove the chicken from the grill or oven and let it rest for 5 minutes.
Garnish with chopped cilantro and serve with lime wedges.