A little more information please!
What kind of stain? Metallic, algae or just lack of maintenance as the boat sat in the water? Salt water or fresh? Is the boat out of the water on a trailer or cradle?
If its metallic there is a product called FSR (Fiberglass Stain Remover) you can get at any marine store (I have not looked for it here) that will take it off chemically in about 20 minutes. Be carefull and wash your hands a lot. It will take the hide off. Have not tried AOL for anything drastic but it does work
If its a plant stain vs plant life I just used the Collinite #920 cleaner with decent results. Plant life takes a scraper or green pad first.
If the boat is out of the water, well and good.
If you are going to try it in the water, safety first! Things powered by electricity seem to have a natural affinity for mixing with water and producing the smell of bad BBQ, and it always takes less than you think. There are also a group of people around who frown about mixing certain chemicals with public water supplies.
Fiberglass gel coat is generally pretty resistant to deep stains unless you have other issues. Like your car, tread lightly first. You can damage the gelcoat and then it gets ugly