Think it cost around $600 to get a new plastic window in my 2002's top.
The shop that did the work had good word of mouth and when I talked to one of the owners he was enthusiastic about doing the replacement. Didn't sound negative or discouraging at all.
The plastic window was the heavy plastic indistinguishable from the factory stuff.
You can get a new top with the plastic rear window. I did after some years after getting the new window sewn in and the top developed a leak.
Cost me around $1400 installed. Same place that replaced the window replaced the top. I went with GAHH top, same color as the factory top (metropole blue), with the extra lining, etc. The car looked the same -- and had the same diminished interior noise -- after the new top was installed. The old top didn't look that bad really it just developed a leak about center of the top due to I guess age.