In a large bowl, combine the soy sauce, honey, rice vinegar, grated ginger, red pepper flakes, and black pepper. Whisk until well blended.
Add the chicken thighs to the marinade, ensuring they are well coated. Cover and refrigerate for at least 30 minutes, or up to 2 hours for more flavor.
Heat the vegetable oil in a large skillet over medium-high heat. Add the chopped onion and sauté for about 3-4 minutes until softened.
Remove the chicken from the marinade (reserve the marinade) and add it to the skillet. Cook for about 6-7 minutes on each side, or until the chicken is browned and cooked through.
Pour the reserved marinade into the skillet and bring to a simmer. Cook for an additional 2-3 minutes until the sauce thickens slightly.
Remove from heat and let the chicken rest for a few minutes. Slice the chicken and serve it drizzled with the sauce, garnished with sliced green onions and sesame seeds.