Here is what I have now based on this thread. https://magick.codeplex.com/discussions/528909
I'm still getting white backgrounds though.
MagickReadSettings settings = new MagickReadSettings();
settings.Format = MagickFormat.Eps;
settings.ColorSpace = ColorSpace.RGB;
settings.Density = new MagickGeometry(72, 72);
using (MagickImage img = new MagickImage(fileName, settings))
{
//tried all of these
img.BackgroundColor = Color.Transparent;
img.Transparent(new MagickColor(Color.Transparent));
img.Alpha(AlphaOption.Transparent);
img.Format = MagickFormat.Png;
byte[] bytes = img.ToByteArray();
Stream s = new MemoryStream(bytes);
s.Position = 0;
return s;
}