A "big boy" is a heavy boy. He could be tall and heavy, or it might just be a nice way of saying that he's fat.
A "tall boy" could be big, but when he stands up, his head is higher than other kids his age.
Finally "big boy", when talking about very young boys, could be a way of making a distinction between a baby and a toddler, a toddler and someone who can use a toilet, or a teenager and someone who understands that he doesn't know everything. :-)
Not necessarily. You correctly built ”mal-granda” but many would say there's a ”neutral zone” between big and small. So there is a difference between ”ne granda” and ”malgranda.”
To me this sounds like „the boy is not big. He is small.“ (with a missing „li estas malgranda“) How is that related to the exercise? What are you trying to express?