Preheat oven to 350 degrees F (175 degrees C). Grease 24 muffin cups, or line with paper muffin liners.
Combine 1 1/2 cups whole wheat flour, all-purpose flour, 1 1/2 cups raw sugar, pumpkin pie spice, baking soda, and salt in a large bowl. Mix eggs, pumpkin, and oil in a small bowl. Stir egg mixture into flour mixture until just moistened; fold in apples. Fill prepared muffin cups 2/3 full.
Combine butter, 1/2 cup raw sugar, 1/4 cup whole wheat flour, and cinnamon in a small bowl; sprinkle over muffin batter.
Bake in preheated oven until golden and a toothpick inserted in the middle comes out clean, 18 to 22 minutes. Cool for 5 minutes before removing from muffin cups to wire racks.