Preheat oven to 400°F (200°C). Line a 9x13 inch baking dish with parchment paper or lightly grease with cooking spray.
Pat salmon fillets completely dry with paper towels. Season both sides with salt and pepper, then arrange in prepared baking dish.
In a small bowl, whisk together honey, soy sauce, lime juice, minced garlic, grated ginger, sesame oil, and red pepper flakes if using.
Pour about two-thirds of the glaze over the salmon fillets, coating evenly. Arrange pineapple chunks around and on top of the salmon.
Bake for 12 to 15 minutes until salmon flakes easily with a fork and reaches 145°F internally. Optionally broil for last 2 minutes to caramelize.
Remove from oven and let rest for 3 to 5 minutes. Drizzle remaining glaze over top, garnish with fresh cilantro, and serve with lime wedges.