I normally keep my cover letters short and sweet. I try to have the initial sentance or two customized for the company in question, and put my portfolio link fairly early on. I know if I were to get a cover letter, I'd click on the links first, and not read the letter till I saw how good the art was.
Just be sure to mention, your name, the company's name, the position you are applying for, and a link to your artwork (if it's an art position).
One thing I do, is make the subject line of the email, the postion, with my name in it. Character Artist: Ben Mathis
This way they can easily find it in their inbox at a later time.