In a bowl whisk together the flour, baking soda and salt. Set aside.
In another bowl add the peanut butter, butter, granulated sugar and dark brown sugar. Using an electric mixer or a wooden spoon , mix well until creamy.
Incorporate vanilla extract and eggs one at a time. Gradually add flour mixture, and mix until just combined.If the batter is too soft to roll into balls, refrigerate for about 30-60 minutes
Preheat oven to 350 F (180C). Line 2 baking sheets with parchment paper.
Take equal portions of dough using an ice cream scoop and form into balls. Roll them into sugar and place on the prepared baking sheets.
Use your thumb to make an indentation into the center of each cookie.
Bake until slightly golden for 10-12 minutes. Transfer cookies to cooling racks to cool completely. While still warm press again the center of each cookie if necessary
While they cool prepare the chocolate ganache. Heat the cream in a small saucepan. When the cream just begins to boil at the edges, remove from heat and pour over the chopped chocolate. Let sit one minute, then stir until smooth. Let it cool for 5 minutes before filling the cookies.
Fill the cookies with chocolate ganache and let it set before serving.They can also freeze well up to 2 weeks.