In a medium mixing bowl, whisk together the coconut milk, maple syrup, vanilla extract, lime juice, and sea salt until smooth and evenly combined.
Add half of the chia seeds to the mixture and whisk vigorously for 30 seconds to distribute them evenly throughout the liquid.
Let the mixture sit at room temperature for 10 minutes, then add the remaining chia seeds and whisk again for another 30 seconds to prevent clumping.
Divide the pudding mixture evenly among 4 serving jars or bowls, cover tightly with lids or plastic wrap, and refrigerate for at least 4 hours or overnight until the chia seeds have absorbed the liquid and the pudding is thick and creamy.
While the pudding chills, toast the coconut flakes in a dry skillet over medium heat for 2-3 minutes, stirring constantly, until golden brown and fragrant. Remove from heat and let cool completely.
Before serving, give each jar a good stir to reincorporate any settled liquid, then top with fresh pineapple chunks, mango chunks, and a generous sprinkle of toasted coconut flakes.