In your cover letter, that is the place to expand upon the information in your resume; you want your cover letter and resume to work with each other to paint a complete picture of you. In your specific instance, given the information you provided, I would put the list of languages on your resume, and then in your cover letter say something along the lines of "As you can see on my resume, I am familiar with both Java and C#.Net. My coursework has focused primarily on Java, but I have also created a basic Patient Administration System using C#.Net as part of a semester-long project." That's it.
Stuffy, overly formal language on resumes is out. It’s wiser nowadays to use direct language. Beware of boilerplate phrases that have lost their meaning and that can be replaced with expressive words that say something specific about you.
LANGUAGES ON RESUME SAMPLE RELATED ,