Marinade: Place scallions, onion, chile pepper to taste, lime juice, oil, brown sugar, allspice, cinnamon, nutmeg, salt, and thyme in a blender. Process until smooth. Place chicken in a 9x13-inch nonreactive baking dish (see Cook's Note) Rub 2/3 cup of the marinade onto both sides of the chicken. Transfer the remaining marinade to a small bowl, cover, and refrigerate. Marinate the chicken in the refrigerator for 2 to 24 hours.
Twenty minutes before you're ready to grill, soak wood chips (if using) in a bowl of water. Transfer the wet wood chips to a smoker box, allowing as much water as possible to drip back into the bowl.
Place the smoker box under the grill above the burner. Close the lid. Heat the grill to medium-high until the chips smell smoky and smoke begins to billow from under the lid, about 15 minutes. Don't worry if the box catches on fire.
Grill the chicken, turning and basting with the reserved marinade, until cooked through (175° to 180° degrees), about 20 to 30 minutes total, depending on the size of the thighs. Discard any unused marinade.
Cook's Note: You can control the heat of this dish by discarding the membranes that hold the seeds, which are the spiciest part of chile peppers, along with the seeds themselves. Be sure to wash your hands thoroughly after handling hot peppers or wear rubber gloves. You can substitute a jalapeno pepper for the habanero pepper, if desired.
Cook's Note: A nonreactive dish is necessary when marinating foods with acidic ingredients, such as lemon, lime, or vinegar. The acid in the marinade can react with "reactive" dishes or pans, such as aluminum and cast-iron, and impart an off color and/or off flavor in the prepared foods.