Being a canoe I assume it will not be in the water all the time so gel coat is water proof enough. Gel coat after many years will admit some moisture which can develope into a problem for say a keel boat but not a canoe.
You will have trouble gettign a nice finish painting gel coat on. It would have to be sanded and buffed way more that it is worth. A pint of single epoxy paint would be about $30 and would come out nice and shiny.
Most epoxy paints are for use above the water line, but again if it is only going to be submerged for short periods that is probably OK. This is a learning experiment right?