In a bowl combine the whole wheat flour, all-purpose flours, baking powder, baking soda, salt, cinnamon and nutmeg. Set aside.
In the bowl of a stand mixer fitted with a paddle attachment, or in a large bowl with a hand-held mixer, beat the butter, brown sugar, honey and vanilla until pale and creamy, scraping down the bowl as needed. Add the flour mixture in 4 additions, alternating with the heavy cream. Scrape down the bowl between each addition.
Divide the dough in two and shape into 2 rectangular disks. Cover with plastic wrap and chill for at least 2 hours and up to several days.
When ready to bake, preheat oven to 350F/175C. Line a sheet pan with parchment paper.
On a lightly floured surface, roll one disk of dough out at a time into a rectangle about 1/8-inch thick. Use a sharp knife or pastry wheel to cut the dough into roughly 3-inch squares. You may want to use a ruler (I did).
Place the squares onto the prepared sheet pan 1/4 inch apart. Sprinkle with coarse sugar, if using. Bake until edges just begin to turn brown, about 12 minutes. Let cool 5 minutes on the pan, then transfer to a wire rack to cool completely.
Graham crackers can be stored in an airtight container at room temperature for up to 1-2 weeks.