The place I got it done was called Rainbow Upholstery in Lock Haven, PA. I don't think they have a website, but the guy has been doing upholstery for 30+ years... Here's a link to google maps so you can plot it yourself:
Google Maps
The stock boxster window is heat sealed (glued/melted?) in place as well as sewn, this replacement window is just sewn in. The two places that recommended this shop are Black Walnut Autobody (they work on the high end stuff in the area) and European Imports, an independent shop that does porsche work, where I had my PPI done on my car before I bought it. I figured if both of them recommended it, then they probably knew what they were doing as those shops regularly have cars a LOT nicer than the ol' box in their shops
I'm sure that if you were going to have it melted/glued as well as sewn, it would cost more, but I figure that the miatas have sewn in windows, and they regularly hold up at least 5 years or more, by the time this stitching fails it will be time for a new top anyway.