Line 36 miniature muffin cups with paper liners.
In a microwave safe bowl, melt about one third of the bittersweet chocolate chips in 30 second increments, stirring in between, until chocolate is melted. Be sure not to overheat the chocolate otherwise it will burn and seize up.
Spoon the chocolate into the muffin cups to just coat the bottom of each cup. Place tins in the refrigerator or freezer for 10 minutes to set.
In a small bowl, mix together flour, peanut butter, vanilla, salt, miniature chocolate chips, and sweetener (maple syrup, honey or brown sugar).
Add 2-3 tablespoons of milk, just until you reach a cookie dough consistency.
Make small balls of dough, about 1/2 teaspoon big, and place on top of each chocolate layer. Lightly flatten the cookie dough balls with your finger so that they are not taller than the muffin well.
Then, melt the remaining chocolate in the microwave. Spoon the remaining chocolate over the cookie dough balls. Allow to set in the refrigerator or freezer.
Thaw before serving.