In a large bowl, mix together the flour, baking soda, and salt; set aside.
In the bowl of an electric mixer, add butter and beat with the paddle attachment until smooth. Scrape the sides of the bowl as necessary to evenly cream it.
Add the sugars, sifted cocoa powder and chipotle peppers and mix again at medium speed until light and fluffy, about 1 minute.
Add eggs, vanilla and water. Beat at medium speed until combined, about 30 seconds.
Add slightly cooled melted chocolate and mix again, scraping bowl to evenly mix everything.
Add the flour mixture, scraping sides and bottom of the bowl as necessary. When well incorporated, add the chips and mix briefly, about 5 seconds.
Refrigerate the dough in the bowl until cool and fudge-like, but not solid, for approximately 1 hour. You can use an ice cream scoop to create large, even sized cookies. These cookie-dough balls can also be frozen at this point, and baked right from the freezer whenever the need arises.
When ready to bake, press the tops of the cookie dough-balls into the sugar, and then top with 2 to 3 pieces of dark chocolate chips.
Place onto parchment-lined baking sheets, allowing space for the cookies to spread.
Bake for 12 to 14 minutes.
Remove the cookies from the oven when they are still a little underdone. Slide the parchment paper with the cookies onto a cooling rack and allow to cool before removing from parchment
