In a small bowl, combine soy sauce, balsamic vinegar, honey, garlic, red pepper flakes, and ginger and mix well. Add chicken thighs and chopped onions to a large bowl. Pour half of the marinade (⅓ cup) over the chicken, covering all the meat. Marinate at least 2 hours, or as long as overnight. Reserve the remaining marinade for later.
To Bake in Air-fryer: Preheat air fryer to 400 degrees. Coat inside basket with cooking spray. Remove chicken from marinade and transfer to the air fryer basket. Cook in batches about 12 minutes total, turning halfway until cooked through in the center.
To Cook in Oven: Preheat oven to 375 degrees. Place chicken thighs in a baking pan coating with cooking spray. Bake uncovered for about 25 minutes until cooked through in the center.
Meanwhile, place the remaining marinade in a small saucepan and cook over medium-low heat until it reduces slightly and thickens, about 1 to 2 minutes.
To serve, drizzle sauce over the chicken and top with scallions, if desired.