Most upholstery places can sew in a new window. I asked a local one about the cost to redo the window on my Miata and it was something like $125. The rest of the top is getting old so I am going to save up for a new one.
No you do not have to replace the top to replace the plastic window. Call around, unless you plan to do it yourself, and get some estimates. I think it may be around $100-150 to have it done professionally.
You can replace the window without replacing the top but the top will have to be undone in places to do it. I described part of the procedure in this post: replacing rear vert window , then there was a post about a novice replacing a top that had some other good replies. the top is un-tacked for the first 6-9 inches along the bottom to access the tacks attaching the bottom of the window, and then the top is un-tacked across the top which entails removing the welt strip (for lacking the proper term), and then pulling the top forward to finish untacking the top of the rear window. The time to do it is now while warm weather is upon us-- makes it much easier.