Who cries saying "it was all a joke"? why?

Although the person who says it was all a joke is only identified as "the boy," we can be confident it is William. We know this because it is William who asks Margot what she is looking at as she stares at the rain. Later on, when "the boy" addresses her:

Then, for the first time, she turned and looked at him.

William seems to have a special hostility to her and react to her look reading in it her desire for the sun. He responds to her look out of his envy that she has experienced something he hasn't. When he says the sun coming out is a joke, he wants to deny her the pleasure she is anticipating. William is the one who orchestrates locking Margot in the closet so that she misses the hour of sunlight.