The following thoughts are off the top of my head. Use with caution.
A 1,500 pound boat must displace 24 cubic feet of water to stay afloat. You probably don't want' your pontoons completely submerged, so plan on them displacing at least twice as much space, or about 24 cubic feet per pontoon. If they are 2' wide, they'll need to be at least 12' long and 2' high. ... Unless you plan on bumping into rocks, docks and hard things, the main consideration for covering the wood is to make it water tight. I suppose you could use that aerosol rubber coating spray they advertise on TV all the time, but I think fiberglass would be a much better choice. Keep in mind that no matter how hard you try, the insides of the toons will probably get wet sooner or later. It would be best to protect the wood by fiberglassing both inside and outside. ... The biggest structural challenge for the pontoons will be the force of the water trying to push the two long sides and the bottom in. A simple solution would be to place wooden reinforcements every 2' or so inside the length of the toons. I'm visualizing an inverted triangle with the points truncated to fit flush against the sides and bottom. I'm sure there is much more I haven't thought of, but maybe this will give you a sense of the magnitude of the engineering task you are undertaking. ... Good luck.