Sift the brown rice flour and almond flour into a mixing bowl. Add the baking soda and baking powder, and whisk to combine. Set aside.
In the bowl of a stand mixer with the paddle attachment, beat the butter until light and creamy, about 1-2 minutes. Mix in the peanut butter. Mix in the honey, the eggs, and the vanilla, and beat until creamy, about 30-60 seconds, on medium-high speed.
Turn the mixer to low and add the flour mixture in increments. Mix until combined, scraping down the bowl as needed. Fold in the chocolate chunks. Refrigerate the dough for 1 hour. (The dough will be very wet.)
Preheat the oven to 350°F. Line a sheet pan(s) with parchment paper or a nonstick mat.
Drop the dough by large spoonfuls onto the prepared pan(s), leaving space between the cookies because the dough will spread significantly.
Transfer to the oven and bake for 9-10 minutes, until browned around the edges slightly but still gooey in the center. If you want to salt the cookies, remove them from the oven halfway (after the dough has flattened), add the salt, and continue to bake.
Cool on baking sheet 2-3 minutes and then transfer to wire rack to continue cooling. Store cookies in an airtight container. Enjoy!