I love names with water meanings, and even though this wouldnt be my first pick for a boy, I wouldnt say "what were his parents thinking?!" if I met someone with this name.
I would definitely spell it
Brook for a boy. No "e".
Also, an option that might eliminate the feminine association is to use the name
Brooks instead. That is traditionally only used for boys. In fact, I've met a guy with this name.