Preheat your oven to 375°F (190°C) and line a standard 12-cup muffin tin with paper liners or lightly grease with cooking spray.
In a medium bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, nutmeg, and ground ginger until evenly combined.
In a large bowl, whisk the melted butter and sugar until completely incorporated. Add eggs one at a time, beating well after each addition. Stir in vanilla extract and Greek yogurt until the mixture is smooth.
Gradually fold the dry ingredients into the wet mixture, stirring just until combined. Be careful not to overmix.
Gently fold in the diced apple, pear, and crystallized ginger pieces. For optimal distribution, consider tossing the fruit pieces in 1 tablespoon of flour before adding to prevent them from sinking.
If using streusel topping, combine the flour, brown sugar, and cinnamon in a small bowl. Work in the cold butter using your fingertips until the mixture resembles coarse crumbs. Stir in the chopped crystallized ginger.
Divide the batter evenly among the prepared muffin cups, filling each about ¾ full. If using streusel, sprinkle it generously over each muffin top.
Bake in the preheated oven for 22-25 minutes, or until a toothpick inserted into the center comes out clean or with just a few moist crumbs. Rotate the pan halfway through baking to ensure even browning.
Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.