When you open the EPS in preview does the logo have a white background or a gray background?... if it has a white background it means it is not transparent for whatever reason (such as there is a white box in the actual logo)...Anyhow, in Preview you can do an Instant Alpha Selection (select tool, click and drag, press delete)
However, I think it may not work with an EPS, which is vector.... Only with raster images, in which case you would have to save as a PNG, PSD, TIFF, etc...


Message was edited by: C.R. (posted before I was done)