Well we all know that Will Hunting is the name of the main character in this movie, so it makes sense that it's in the title. But the moment you throw "Good" in front of his name, it messes with the meaning.
After all, we can probably agree that Will is actually "hunting" in this movie because he's searching for a way to move on with his life and make decisions about his future. But the "good" also makes us wonder if we're looking at a person who has "goodwill" while he's in the act of hunting. Or, if he's on the hunt for a person with goodwill.
So now we have a title that suggests on one level that Will Hunting is good and that Will hunts with/for goodwill. In both cases, the title is accurate because it reminds us that there are good and bad ways to hunt for meaning in life, and Will is following the good one (most of the time).
On another level, the title is just saying, "Give Will a chance because he's a good dude."