In a large bowl, stir together 3 tablespoons of oil, the lime zest, habanero, 1½ teaspoons salt and 1 teaspoon pepper. Transfer 2 teaspoons of the mixture to a small bowl and set aside. To the remaining oil-zest mixture, whisk in the lime juice, bouillon and ¼ cup water. Add the chicken and onions and toss. Cover and let marinate at room temperature for 1 hour or refrigerate up to 2 hours, stirring once.

Remove the chicken from the marinade and pat dry with paper towels. Set a colander over a large bowl and strain the onions, reserving both the marinade and the onions.

In a large Dutch oven over medium-high, heat the remaining 1 tablespoon oil until barely smoking. Add the chicken, skin side down, and cook until well browned, about 4 minutes. Transfer to a plate and pour off and discard all but 1 tablespoon of the fat. Set the pot over medium heat and stir in the onions and ¼ cup water, scraping up any browned bits. Cover and cook, stirring frequently, until the onions are softened and lightly browned, 15 to 20 minutes.

Stir the reserved marinade into the onions. Return the chicken, skin side up, to the pot, nestling the pieces in the sauce, then pour in any accumulated juices. Reduce to medium-low, cover and cook, stirring occasionally, until a skewer inserted into the thickest part of the meat meets no resistance, about 25 minutes.