Heat water in the microwave until it’s very warm, like hot bathwater. (This takes about 45-60 seconds in my microwave). Add the yeast and brown sugar, stir and let sit for 5 minutes until frothy.
While the yeast is proofing, add 3 1/2 cups flour and salt to a stand mixer fitted with the paddle attachment. (Alternately you can use a wooden spoon and a large bowl, it just uses more elbow grease!) Stir together the flour and salt.
Turn the mixer on low and slowly pour the yeast mixture into the flour mixture. Mix until dough has formed, then mix for another minute. If the dough is too sticky to handle, add up to another 1/2 cup of flour (I had to add the extra 1/2 cup). The resulting dough will be slightly sticky but you should be able to touch it with only minimal transfer to your hands.
Spray another large bowl with cooking spray and then transfer the dough to the new bowl. Spray the dough with cooking spray and cover with plastic wrap. Let sit until doubled in size, about one hour.
Bring a large pot of water to boil on the stove.
Once dough has risen, turn it out onto a lightly floured surface. Divide the dough into 12 equal parts and roll them into balls. Let them sit for 5 minutes.
Once the water has boiled, line two cookie sheets with silpat baking mats or spray them with cooking spray. Add the honey to the water and stir.
Preheat oven to 350°F.
Pick up each dough ball and press two fingers through the center, creating the hole of the bagel. Boil for about 45 seconds, flipping once. (I boiled two bagels at a time.) Remove from water with a slotted spoon and place on prepared cookie sheets. Continue until all bagels are boiled.
Beat the egg in a small bowl and brush a little on the top of each bagel. Stir the granulated sugar and cinnamon together in a small bowl and sprinkle a little on top of each bagel.
Bake bagels for 15-20 minutes, rotating pans halfway through baking, until they start to turn golden brown.
Serve the bagels warm from the oven, or cold, or toasted. Store in an airtight container; they are best eaten within 2 days but you can freeze them for up to one month.