If it's for a cover letter, and you're seeking a particular position, state the position and how much you, with your experience, skills, etc., would contribute to the position and the company:
"...before seeking the position of [insert name of position] with [insert name of company.]"
If you do a simple search online there are lots of great, free examples of cover letters and letters of interest that could even be specific to your particular field. Most local libraries have resume-building workshops too.
To answer your question specifically, I would choose "with" because it implies 1) that you are a good match for that company and its mission (whereas "at" or "in" implies a vertical relationship) and 2) you are a "team player/investor" who contributes your own wealth of knowledge, energy, and labor to the shared goal of the company's success.