Preheat the oven to 350 degrees F (175 degrees C). Grease two 12-cup muffin tins or line cups with paper liners.
Combine flour, sugar, baking powder, salt, cinnamon, nutmeg, and ginger in a large bowl. In a second bowl, whisk together pumpkin puree, soy milk, oil, and agave nectar until evenly blended. Make a well in the flour mixture and pour in pumpkin mixture; stir just until batter is combined. Fold in chocolate chips.
Spoon batter into the prepared muffin cups, filling each 3/4 full. Bake in the preheated oven until tops spring back when lightly pressed, 18 to 20 minutes.
Meanwhile, cream coconut cream, vanilla extract, and confectioners' sugar in a bowl until creamy. Refrigerate until use.
Remove cupcakes from the oven and cool in the tins for 5 minutes. Transfer to a wire rack to cool completely, about 20 minutes.
Frost cooled cupcakes with coconut cream frosting and sprinkle with a thick layer of coconut flakes.
