For the magic squares problem, do NOT ask the user to type in n² numbers. It's hard to test this without making typos or creating an input panel that has a nice GUI.

What I mostly want to see is whether you can write isMagic() and what helper methods you choose to write in order to get isMagic() to work. So, your code ought to look like this:

public static void main(String[] args) {
  int[][] ints = { { 16,  3,  2, 13 },
	           {  5, 10, 11,  8 },
                   {  9,  6,  7, 12 },
                   {  4, 15, 14,  1 } } ;
  Square sq = new Square(ints);
  System.out.println(sq.isMagic());
}

If you insist on reading user input instead of entering a square into the code, that's fine, but understand that it will be time-consuming and won't get you any extra credit.