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I haven't replaced my top (Boxster) but I have looked into both options because I have a small tear in my window. The Porsche tops cost a bit - roughly $3k installed at a dealer. I expect the top iteslf runs up toward $1000. The best aftermarket top seem to be from the Robbins company (~$600 for a Boxster). They use the same materials and re-use the same frame.
I went to a local shop (that I was impressed with after speaking with the owner and that does this work for a lot of local dealers) and a replacement window would be $600-$700. A replacement top would be about $1700 installed.
The risk with a window is that there always a possibility of it leaking (I don't know how much of a risk). They may be able to use some of the new plastics that are less likely to scratch, though.
If the rest of your top is good, I'd say go for the window and replace the top some other time when it starts looking worn.
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