If it's the MIT media lab you really want, which always seemed like an amazing experience, then figure out a way to visit, meet the people, and understand what they are doing.

Doing your own projects/research and publishing them would help to get your name out there. I'm not an 'academic' by any stretch, but that's what I would do if there was a job/opportunity I really wanted.

Do something amazing and doors will open.

Apply through the 'machine' and there will always be hundreds of people competing in the GPA/undergrad arena, and chances are they all have a better GPA than you.