Is it even worth applying? Biomedical programs NYC

[gengal]

Hiya all!
I am debating about if I should apply this coming application season. 
I plan to apply to Biomedical PhD programs in and around NYC surrounding molecular and structural biology. We all know that admission is narrow, so given my current situation, should I prepare to apply?
* 2.5 years of biochemistry research (ongoing)
* 6 months of Microbiology research (ongoing)
* 1 publication
* another publication on the way
*current gpa 3.5, major gpa is 3.2
* I did a pass/fail option once for organic chemistry 1 (got a fail, then retook the class and got an A), then did another pass/fail option for gen bio 2 (I got a pass, then retook and got an A), got a C in gen bio 1 (retook and got an A)
* I did a withdraw for physics II (retaking currently)
* I took a lot of biology electives, such as microbiology, anatomy and physiology, and genetics (all a B or A grade). 
* Biochemistry major, Anthropology minor
* Taking biochemistry 1 at the moment and I worry I will not do well, the best I will do is a C or a B- , so I want to retake it next semester for a better grade. 
* I also am studying currently for the biology GRE. 

Basically, I'm all over the place. I could really use some guidance. I want to get to a good PhD program right after my undergrad. 
I have an idea of where I'd want to apply, like Sackler (NYU), Columbia, Rutgers, Weill Cornell, Mount Sinai. 

Does anyone recommend me to apply, take a gap year, or get a Master's first? I don't know what is right. Anyone with experience in this would help a bunch!

Thanks in advance.