Epoxy resin will degrade from direct exposure to UV light, so it is not a good choice for replacing a portlight on your boat. Not to mention that even clear epoxy would never be as clear as the portlight you are replacing-- you would get light through it (at least for a while, before it started yellowing from the sun) but you wouldn't be able to see things clearly through it.
I would buy lexan or another high quality polycarbonate resin panel and cut it to size using a router with a sharp bit. If you use a thin panel, sandwiching the lexan between two thin sheets of plywood with double-sided tape will prevent the lexan from flexing and cracking when hit with the spinning router bit. Just trace the shape you need on the top piece of plywood and then follow that line with the router. If you don't think you can control a router that precisely, make a template out of wood and then use a router bit with a bearing on it to follow the template. Lexan comes in a wide range of sizes and thicknesses, many of which are sold at Lowes and Home Depot, so you should be able to find what you need for your application without much trouble.