I did mine but unfortunately don't remember the thickness of the plexiglass. 1/4 maybe? I did use plexiglass that I had cut at a glass shop, I used a darker tint when I replaced. Removing the frame was not hard but getting the window out of the frame was a bit of a mess. They used a lot of black sealer when the boat was built. I had the frames powder coated and the finshed product looks good I think. You will need to get the rubber "gasket" material too along with the plastic stuff that slides in the channel to hide the fastening screws. I rebuilt the side windows at the same time.
Update - I just was looking around to see if I had kept the the old windows but it appears not. At the same time I replaced my windows I replaced the plastic panel over my instruments and I still have that. It is 1/4" I don't think the windows were any thinner. Perhaps someone will have more info for you.