In a small bowl with an electric mixer, beat together cream cheese, sugar, and vanilla extract together until smooth. Set aside.
Preheat oven to 350 degrees F. Line a muffin pan with 12 muffin liners or spray well with nonstick spray. In a medium mixing whisk together the whole wheat flour, baking powder, baking soda, salt, ground cinnamon, nutmeg, and ginger. Set aside.
In a large mixing bowl mix together the oil, sugars. eggs, and vanilla extract until combined.
Fold the dry ingredients in with the wet ingredients just until combined and then fold in the shredded carrots. Do not over-mix.
Add 2 heaping tablespoons of carrot cake batter to each muffin liner, then add 1-2 tablespoons of the cream cheese mixture to the center of the carrot cake batter. Divide the remaining batter to the tops of the cream cheese mixture. Gently spread the batter with a spoon to cover as much cream cheese mixture as possible.
Bake muffins for 18-20 minutes or until a toothpick inserted comes out clean. Let cool for a few minutes before transferring to a wire cooling wrack. Frost with leftover cream cheese mixture, walnuts, or leave them plain. Enjoy warm or cold!