My first piece of advice: ask the professor with whom you're currently working 1) what he/she thinks of your current qualifications, and 2) what he/she thinks you can do to increase your competitiveness as an applicant. He/She presumably sees tons of applications and can give you a strong sense of how to spend your year "off" in order to maximize your chances of being offered admissions.
Another thing: there's maybe not much you can do with your GPA, but you can definitely boost your GRE scores. 96%/84% is very good, but, potentially, you could score a 99%/99%. It's no mystery that the closer to perfect your GRE score is, the better your chances are.
LoRs: Audit a class, volunteer in another lab.
Then: Try to publish a paper. Let your current PI know that you'd like to try to make that happen. He/She would likely be thrilled to have someone else to do some heavy lifting and may even provide a lot of the support that you'll need in order to get it done (e.g., give you a reading list, give reliable critical feedback, etc.). If you can publish a paper, it makes the 3.33 kind of fade to the background a little bit more. Also, present at some conferences. Society for Neuroscience is a good one.
Finally: Only apply to schools where you think you are a good fit. I think "fit" means that the program's requirements work for your style (e.g., if you don't like to be in classes, don't apply to a school with a lot of required classes), and there is at least one PI there who does something you think you'd love to spend 5-6 years doing. Ask your current PI about which programs he/she thinks will work for you given your style and interests. For me, it was kind of tempting to try and get in to illustrious programs (I guess to feed my ego), but in the end it became clear that "fit" was the most important variable (for me and for the programs) and I ended up wasting some time applying to schools where I wouldn't have been happy or successful.
Enjoy your application process! It can be tiring but very fun.