You have two options
1)Get it repaired
This will involve patching the hole with a special compound. It is similar to bondo for steel. Then a dye on top of the repair and surrounding vinyl to blend in the color. Although this may be the most cost effective route it may prove to be the worst option for a boat. A boat seat sees much more abuse than a standard vehicle interior. Sun, water, and people stepping on the seat may cause the repair to crack or fade to a different color than the rest of the vinyl. My advise would be to call your local vinyl repair guys (there are not many of them... only 2 in Sacramento Valley) and let them know your situation and if they will do the repair and guaranty against any of the things mentioned above and for how long.
2)Replace only the damaged section
Depending on the type of stitching around the damaged area, just the damaged panel of vinyl can be replaced. Most upholstery shops will want to see the seat before they quote you a price. I'm not sure what seat it is but even if you have to unbolt it to take it in I would to save yourself the hassle of towing the boat around or them storing it while the repair is done. The big thing to make sure of is to take your time in finding the correct vinyl. You may need to contact the boat manufacture to order a yard of the material if it isn't a very standard color. OEM vinyl may be an extra $50 but in some cases it is the only way to go.
-My opinion.. Order OEM vinyl (if needed) and replace the section. Repair should be $100-250 depending on size of section.