What is best for your brakes when stopping at the bottom of the hill?
In terms of wearing out the brakes, they will wear less when you brake at the bottom.
When you descend a hill you have a fixed amount of energy to lose, and when you descend at a higher speed, a larger proportion of that energy is lost to wind resistance.

Practically however, brake pads/blocks tend to last a long time and are cheap to replace, wear is not really something to consider too much.  It's better to descend safely at a speed you feel comfortable with.