Get a handle to the errorbar
object. It has two children, corresponding to the data plot and error bars respectively. Then you can set the color of each separately.
h = errorbar(x,y,e) %// a color spec here would affect both data and error bars
hc = get(h, 'Children')
set(hc(1),'color','b') %// data
set(hc(2),'color','g') %// error bars