4" square filters come as gelatin filters, polyester, and acrylic, as far as I know. I know B+W and Heliopan make glass filters in frames to fit 3x3" (really expensive last I checked), but I'm not sure they make them in 4x4".
I don't necessarily think that acrylic is a bad choice, but I'd be a little concerned about flatness if they aren't manufactured for optical use. The Lee and Hi-Tech filters are supposed to be good, as far as new acrylic filters go. I know that my Ambico ND filters and Cokin ND filters and ND grads are slightly warmer than neutral, but the Lee filters are supposed to be much better in this regard, if you're shooting color.