The most important thing to remember is you can't be hired if you don't apply. I'm a freshman in university now and had my internship between Junior and Senior year of HS, and I certainly wasn't qualified for it when I started, though the hiring company seemed to disagree ;) Having the audacity to ask was what got me that job, and it has lead to plenty of opportunities since.
To get back to your question, the answer is "it depends". Is the team you're going to be working on essentially looking for a new employee they'd like to hire post-graduation and have around in the meantime, or are you going to be applying for an internship at a larger company where they might not be focused on coding prowess so much as "smart" and trainable? Either will figure out during the interview process whether or not you're a good fit, and find a place for you to use the skills you have and learn new ones.
To get back to your question, the answer is "it depends". Is the team you're going to be working on essentially looking for a new employee they'd like to hire post-graduation and have around in the meantime, or are you going to be applying for an internship at a larger company where they might not be focused on coding prowess so much as "smart" and trainable? Either will figure out during the interview process whether or not you're a good fit, and find a place for you to use the skills you have and learn new ones.