Preheat your oven to 350 degrees F. Grease baking sheets with non-stick cooking spray and set aside.
In a medium mixing bowl, whisk together the flour, cocoa, baking powder, and salt. Set aside.
In a large mixing bowl, beat together the butter and sugars until fluffy, about 1 minute. Mix in the eggs and vanilla until smooth.
Gradually add the dry ingredients to the wet ingredients. Once combined, stir in the chocolate chips and M&Ms by hand.
Drop cookies by tablespoonfuls onto the greased baking sheets, leaving about 2-inches between the cookies. Top each dough ball with two semi-sweet chocolate chips, 1 green M&M, and 1 red M&M. (Don't add the white chocolate chips on top, they'll brown.)
Bake for 13-14 minutes until the cookies are mostly set. (They will finish setting up as they cool.) Leave the cookies on the baking sheets for 5 minutes, and then transfer to wire racks to cool completely.
Notes
If desired, add two or three white chocolate chips to the top of each cookie right after the cookies come out of the oven.