They both run the same commands under the hood, so you will end up with the same upgrade either way.

The main advantage of the command-line method is that it makes it easier to see any errors/warnings that might occur, so power-users can quickly fix them. The downside of that is that the specific errors are often confusing/scary, and the GUI method does a much better job of explaining things and how to fix them. The GUI method should be recommended for most people, especially new users.