I would suggest starting with mild detergent then working your way up. Try dish soap, then some oxy clean, then possibly lestoil. If none of this works, then you can try some harsher vinyl cleaner.
I use the Gizmo covers for this exact reason. I just do not like the stains that the leaves and things cause on the bunk ends.
2006 HW256 (previous pup)
2013 Chevy Tahoe
Equalizer WDH 1000#