I have seen people use lexan and make the new window larger than the opening and somehow decoratively screw it onto the opening. THis is a good safety issue too as a breaking wave will have difficulty pushing the window in. If that is a concern of yours.
There is also the car rubber windshield stuff. But that will probably need a window smaller than the opening. and be possible for the above wave to knock it in.
I have heard of the rubber gasket stuff that has offset grooves and allows the window to be larger than the opening.