Preheat oven to 350°F. Coat a 12-cup muffin tin with cooking spray.
Whisk all-purpose flour, whole-wheat flour, cinnamon, ginger, baking soda, baking powder and salt in a medium bowl. Whisk eggs, brown sugar, oil and vanilla in a large bowl.
Dice 1/2 cup pineapple. Shred the remaining pineapple with the large holes of a box grater. Add all the pineapple (along with any juices), apple and carrot to the egg mixture. Mix in the dry ingredients until almost combined. Fold in 1/2 cup coconut, walnuts and raisins. Divide the batter among the prepared muffin cups. Sprinkle with the remaining 1/4 cup coconut.
Bake the muffins until a toothpick inserted in the center comes out clean, 18 to 20 minutes. Let cool in the pan on a wire rack for 10 minutes before serving.
Store at room temperature for up to 2 days or freeze for up to 1 month.
Muffin tin with 12 (1/2-cup) cups