Preheat your oven to 400 F. Grease a 12-well muffin tin with butter or cooking spray.
In a small bowl, combine the cream cheese, vanilla, and honey until smooth. Set aside.
In a large bowl, whisk together the flour, both sugars, baking soda, baking powder, ground ginger, cinnamon, nutmeg, and salt.
In another small bowl, whisk together the eggs, water, and olive oil.
Make a well in the middle of the dry ingredients in the large bowl and add your wet ingredients. Mix together until dry ingredients are fully moistened and no dry spots remain.
Fold in the carrots, cranberries, and crystalized ginger.
Fill each well of the muffin tin with about 3 Tbsp of batter, then top with a large spoonful of cream cheese mixture on the center.
Bake, checking around the 18-22 minute mark with a toothpick. If the toothpick comes out clean, they are done. Cool on a rack and enjoy.