Preheat oven to 450°F. (be sure to preheat pizza stone as well, if using)
For dough: Place water, yeast, sugar, honey, and olive oil in a mixing bowl and gently stir together. Allow mixture to sit for 5 minutes (water should begin foaming slightly).
While yeast mixture sits, sift together flour and salt. Add flour mixture to yeast mixture, ½ cup at a time, until fully incorporated and dough begins to form. Turn dough onto a lightly floured surface and knead until smooth, about 8 to 10 minutes. (dough should spring back when poked).
Form into a ball and place in a lightly greased bowl and cover with plastic wrap or a damp towel and place in a warm area and allow to proof until doubled in size, about 1 ½ -2 hours. Punch dough down and turn onto a clean, lightly floured surface.
Divide dough into two equal pieces and roll each piece into a 14 inch disc, about 1/4 inch thick. Sprinkle baking sheets with a layer of cornmeal. (if using a pizza peel, sprinkle peel with thin layer of cornmeal)
Place crusts into the prepared baking sheets, pierce the surface all over with a fork, and brush with small amount olive oil. Refrigerate until ready to use.
For toppings and assembly: Melt butter in a large skillet, over medium-low heat and add onions. Lightly caramelize onions for 10 to 12 minutes, stirring occasionally. Add sliced apple and continue to caramelize for an additional 6 to 8 minutes. Lightly season with salt and pepper and set aside and allow mixture to cool.
Remove prepared crusts from the refrigerator and top each pizza with 2 ounces of crumbled bleu cheese, half the onion and apple mixture and finish with the remaining bleu cheese.
Bake for 12-14 minutes or until golden brown and crisp. Remove from oven and allow pizza to cool before topping with fresh thyme and cracked black pepper. Slice and serve.