When I read "senior thesis" my eyes glaze over
Despite the fact your academic advisers have convinced you these are really important, most people don't care about them in the real world. Be wary of dwelling on what your topic is and PLEASE do not attach a chapter with your application. Writing a senior thesis has nothing to do with journalism. I'll never open it, and I'll resent you for sending it.
I don't really care what classes you've taken, either
I'm much more interested in what you've done that relates to the skills needed for the position than I am in what you've studied. An interesting Tumblr account, a vibrant Twitter presence, or a personal blog on a topic you are passionate about is 10 times more compelling to me than your course load.
Your college and GPA aren't as important as you think
This may be the biggest blow to you, grasshopper. In general, I don't care about your GPA or whether you went to an Ivy League school, so definitely don't expect this alone to swing open any doors for you. Of all the entry-level people I've hired, the one that went on to have the most successful career in media never finished college. If you are still in college, you should mention where you go and what you study. But the further out of college you are, the less I want to hear about where you went or how you did there.
Follow the application instructions to a T
I often give really specific instructions in the job posting, listing a word limit on cover letters, requesting exactly two writing samples, and noting a firm deadline for when applications are due. This is my first test in how good you are at taking direction. If you send four writing samples rather than two, that doesn't make me think you are overqualified, it makes me think you can't edit yourself or aren't good at doing what is asked of you. Small mistakes like this help me figure out whom to eliminate, so tread carefully.
If you follow these instructions, you should have a good shot at making it to the top of the pile. It might not be long before you're on the other side of the desk, reading cover letters yourself. Good luck.