You should give them more than two weeks, especially since classes have started at all schools by now. After three weeks, you should drop by their office or give them a call/email to say it's rather urgent that they complete your rec ASAP. Most people feel like they are imposing on the prof when they approach them. But as one of my recommenders told me, it is part of their job responsibility to write recommendations for students.
Unfortunately, you are not in a comfortable position since you asked them quite late (not getting down on you--so did I!), so you will just have to sweat it out and keep politely prodding them to get it done.
Good luck!