Preheat your oven to 350. Racks in the middle zone.
Make the cookie dough:
In a mixer cream the butter until it is light and fluffy. Add the powdered sugar and continue to cream, scraping the sides of the bowl a couple times if necessary. Stir in the vanilla extract, salt, and cocoa powder. Mix until the cocoa powder is integrated and the batter is smooth and creamy, resembling a thick frosting. Add the whole wheat pastry flour and mix just until the batter is no longer dusty looking but still a bit crumbly. Don't overmix.
Turn the dough out onto a clean counter, gather it into a ball, and kneed it just once or twice to bring it together into once nice, smooth mass. Place the ball of dough into a large plastic bag and flatten it into a disk roughly 3/4-inch thick. Place the dough in the freezer for 15 minutes to chill.
Rollout and bake:
Remove the dough from the freezer and roll it out really thin, about 1/8-inch. These are called thin mints after all. You can either roll it out between two sheets of plastic, or dust your counter and rolling pin with a bit of flour and do it that way. Stamp out cookies using a 1 1/2-inch cutter (any shape or design you like). Place cookies on a parchment-lined baking sheet and bake for 10 minutes. Remove the cookies from the oven and allow them to cool completely on a wire rack.
Make the peppermint coating:
Meanwhile, prepare your chocolate coating. Using a double boiler, slowly melt the chocolate, stirring occasionally until it is glossy and smooth. Alternatively, use a microwave in short 15-20 second bursts to melt the chocolate. Stir in the peppermint extract. If you think the chocolate needs a bit more peppermint kick, add more extract a drop or two at a time to taste - but don't go overboard.
Finishing the cookies:
Using a fork, gently drop the cookies, one at a time, into the chocolate coating. Flip to coat all sides. Lift the cookie out of the chocolate with the fork and bang the fork on the side of the pan to drain any extra chocolate off the cookie. You are after a thin, even coating of chocolate. Place on a parchment lined baking sheet, and repeat for the rest of the cookies. Place the cookies in the refrigerator or freezer to set. Best eaten straight from the freezer where they will keep almost indefinitely (not that they'll last that long).