This is most likely mold from moisture trapped between the cover and the vinyl. Some air space between the two can avoid this, perhaps some cardboard (if boat is stored in dry area) or as mentioned pvc pipe to provide an air space. Mold can do some weird things, often it's very tough to remove these stains and the products mentioned above may work. Other times it wipes right off.
Personally, I avoid using products containing bleach b/c the bleach can attack the upholstery threads and cause them to fail.
Might also try a strong solution of hydrogen peroxide, good luck.
I'm a firm supporter of vinyl spray paint, I've used it before and when applied as directed had fantastic results even with changing from one color (dark brown) to another color (medium blue).