im confused? you say small boat but then say its for a pontoon (which isn't small)
I have seen some with fiberglass, I even saw one guy do his with pvc and covered with a plastic folding table he just cut down to size to fit.
for a small boat, you might just want to check a welding place and see what it would cost to weld up a frame with aluminum sheet roof. might be $100-$200 but it would last forever and be solid protection.
for the pontoon I would suggest something like this:
http://www.walmart.com/ip/11007577?w...357790&veh=sem
they can be cut found in different sizes and the frame screwed into place