If the boy is still a child, pre-adolescent, he can be described as being beautiful.
He's a beautiful baby/child/boy
sounds perfectly acceptable to my ears. The boy himself might object to being called beautiful once he turns into a teenager, as it is usually considered an effeminate term.
For teenagers and adults, the genderless adjectives good-looking, and attractive are the safest and best-known options. They can be used for young and “mature” people, both men and women.
Good-looking as defined by Oxford Dictionaries (Chiefly of a person) attractive.
Damon looks to be on the fast track towards becoming one of cinema's brightest bad boys. He's a good looking guy who can look brooding with the best of them, bringing to mind James Dean and the young Marlon Brando
I'm tall, slim, blonde and, so I'm often told, a good-looking woman. I know how lucky I am. But there are downsides to being pretty…
attractive (Of a person) appealing to look at; sexually alluring: