Make the Cupcakes: Preheat oven to 350 degrees F. Line a cupcake pan with paper liners; set aside.
In the bowl of a stand mixer, add the flours, sugar, baking powder and salt, and mix together on low speed for 1 minute. With the mixer on low, add the butter, a few cubes at a time, continuing until all the butter has been added and the mixture resembles coarse sand.
Keeping the mixer on low speed, add the eggs one at a time, scraping down the sides of the bowl between additions. Slowly pour in the milk, vanilla and mint extract, and mix until combined. Add the green food coloring and mix until color is evenly dispersed throughout the batter. Increase the mixer speed to medium and beat for 2 minutes, until batter is smooth, scraping the sides of bowl as needed.
Fill the liners two-thirds full (about ¼ cup of batter) and bake for 15-20 minutes, until the centers are set and a toothpick inserted into the center comes out clean. Cool in pan for 10 minutes, then remove to a wire rack to cool completely before frosting.
Make the Frosting: On medium speed, beat the cream cheese, sugar and vanilla extract in a mixer with the whisk attachment until smooth and completely combined, about 3 minutes. Slowly add the heavy cream, scrape the sides of the bowl, then increase speed to medium-high and whip until stiff peaks form.
Assemble the Cupcakes: Pipe the frosting onto the cupcakes, then sprinkle with green sanding sugar and top with green maraschino cherries, if desired. Serve immediately, or store in an airtight container in the refrigerator for up to 3 days.