Preheat oven to 375º Fahrenheit. Chop ⅔ cup cranberries and set aside. Pat chicken thighs completely dry with paper towels then season liberally with sea salt.
In large skillet over medium-high heat, heat olive oil until shimmery. Once oil is hot, add salted chicken thighs to skillet, skin-side down.
Cook approximately 8 minutes or until chicken thighs lift easily from pan. Flip thighs over and cook skin-side up for 2 to 3 minutes.
Add remaining ⅓ cup whole cranberries to skillet. Transfer skillet to oven and roast for 14 minutes.
Remove skillet from oven. Carefully remove chicken thighs and whole cranberries, transferring all to plate to rest.
Return skillet to stovetop over medium-low heat. Add minced shallot to skillet and cook, stirring frequently, until shallots soften, approximately 2 to 3 minutes.
Add chopped cranberries to skillet and stir. Pour in coconut aminos and chicken stock to deglaze pan, using whisk to scrape up any browned bits on skillet.
Add fresh thyme and bring sauce to simmer. Let sauce reduce until thickened, approximately 4 to 5 minutes. Serve sauce warm over chicken thighs and top with roasted cranberries.