Do I have any chance to apply to a graduate school after a bad junior year?
I think you should not worry about the 'junior' days. You are now equipped to apply anywhere.  If you are concerned about not making at the top schools, also apply at say five second choices.  If you get accepted at one or more top schools, you can pass the others. Get best testimonials in your hand so you are ready for the next move up.  Best of luck.