Both epoxy and polyester will do the job well but getting a good quality brand is more crucial as some cheaper blended resins are very poor.
One thing to consider is what kind of canoe you want? thick and strong will suit epoxy better or light and flexible will suit polyester better. Polyester has more flex but lacks strength. epoxy resin has its own strength with no substrate whereas polyester isn’t that strong without other materials to bond too.
I would err on the side of choosing epoxy as the cost increase isn’t a lot with something as small as a canoe, but you will probably end up requiring a 2 part polyester paint to put on top of the epoxy to shield it from UV.