I'm not sure where to apply to be honest, you're going to have to look around. Some schools are more lenient than others. In the end, they just want you to be able to do research well, but they don't want you floundering in graduate courses.
You're also going to need another letter of recommendation. I've only see one school that only required 2 letters.
I'm not trying to discourage you btw, just trying to give you an idea of what I've seen/heard while I was applying last year.
Have you considered doing a masters somewhere, improving your credentials, then applying to a Ph.D program somewhere else? There are some good programs they are set up for terminal masters. This is going to add atleast 2 years to your education, but it would give you a chance to pump out a publication and give you a second chance to gain a strong GPA. Not sure how other feel about this idea; it was my backup plan if I didn't get accepted to a school I wanted to go to.