Proof the yeast by placing it in a large bowl and adding 1 1/2 teaspoons of the brown sugar and the warm water. Stir well and set aside until the mixture bubbles and a slight foam forms on top, about 5 minutes.
Add the remaining 1 1/2 teaspoons sugar and the salt; stir well. Gradually add the flour, 1 cup at a time. Mix the dough until the flour is well incorporated.
Knead the dough until smooth. (By hand this takes about 7 minutes.) The dough should retain a sheen and not appear too floury. The dough should not be sticky, so add flour as necessary. Cover the bowl and set aside to rest in a warm place for 40 minutes.
Turn out the risen dough onto a floured surface. Cut/break off chunks and form into bagels. You can do this by forming a ball and piercing the ball with your finger and spinning the dough around until the hole is the right size.
Or, you can twist the dough into ropes and then twist the rope into a circle. This makes 10-12 bagels.
Place each bagel on baking sheets and set aside in a warm place, uncovered, for 30 minutes.
Preheat the oven to 425 °F.
Fill a large, wide pot about 2/3 full with water and bring to a boil. Using a wide, slotted spooon, drop the bagels in batches into the water; they must not touch. Boil on one side for 2 minutes. Turn the bagels and boil on the second side for 1 1/2 minutes. They should firm and puff up. Carefully remove from the water and drain for 1 minute on a rack. At this point, add whatever toppings you want. (You can skip the draining if you’re in a hurry, the bagels come out fine.)
Place the bagels on baking sheets. Bake for 12 minutes. Turn the bagels over and bake another 7 minutes or until a deep golden brown all over. Remove from oven and cool.