I've long relied on the free Gentium typeface, which has a simply gorgeous, highly readable polytonic Greek font, with diacriticals that I've always found quite easy to distinguish, both on the printed page and on the computer screen. I used to have a custom stylesheet to display all Greek text on the Perseus website in Gentium, because it's much easier on my eyes.
You should also check out the site of the Greek Font Society, which offers some very fine recreations/digitizations of historically significant polytonic Greek fonts, also available for free download. Some of GFS's faces don't even have Latin fonts; their focus really is on high-quality Greek typography, though some of the faces are more appropriate than others for regular running text. The diacriticals in the GFS Didot Classic face, in particular, are extremely pronounced and clear – almost too clear, if that's possible. Their GFS Heraklit face, after an original by Hermann Zapf, is also very nice, with quite distinct diacriticals.
Update: As requested, here are examples of the 3 faces that I mentioned (plus a fourth, GFS Porson). In the document that I captured the image from, the text for all 4 examples was set at 11 points with line spacing set at 14 points.