Preheat your oven to 350°F (175°C). Prepare a muffin pan by lining it with paper cups or greasing it lightly.
In a small bowl, mix together the coconut sugar and cinnamon for the topping, and set it aside.
In a separate medium-sized bowl, whisk together the whole wheat flour, baking powder, baking soda, cinnamon, and sea salt.
In a large mixing bowl, cream together the softened butter and coconut sugar until smooth. Add the eggs, pumpkin puree, and vanilla extract, stirring until combined. Mix in the Greek yogurt until the batter is creamy.
Gradually fold the dry flour mixture into the wet ingredients, stirring gently. Once well combined, carefully incorporate the diced apples.
Spoon the batter evenly into the muffin pan, filling each cup nearly to the top. Sprinkle the cinnamon-sugar mixture over the tops of the muffins.
Bake for 22-25 minutes or until a toothpick inserted in the center of a muffin comes out clean.
Let the muffins cool for about 15 minutes on a wire rack before serving.
Store any leftover muffins at room temperature for 2-3 days, or refrigerate for up to 1 week. For longer storage, freeze for up to 3 months.