Lightly coat a 5-quart or larger slow cooker with baking spray and arrange the chicken thighs in a single layer on top. Drain the pineapple juice from the can into a large liquid measuring cup or mixing bowl. Whisk in the cornstarch. Once smooth, stir in the soy sauce, garlic, ginger, sesame oil, red pepper flakes, and black pepper. Pour over the chicken. Add the pineapple chunks and red pepper.
Cover the slow cooker and cook on LOW for 4-5 hours or HIGH for 1 1/2 – 2 hours, until cooked through.
With a slotted spoon, remove the chicken and vegetable mixture to a plate. Strain the sauce into a small saucepan. Simmer over high until it reduces by half, about 4-5 minutes, stirring very frequently. Add back to the slow cooker with the chicken mixture. Add the water chestnuts and green onion. Stir to combine. Serve hot with cauliflower rice, brown rice, or quinoa.