There is an old, free one that I think still works on most macs.
It is called Dotty Plotter. I wrote it, but no longer support it.
See at ftp.bio.indiana.edu:/molbio/mac/dottyplot.hqx
[SeqApp on mac should also do dot plots, but this software is in
flux, and the dotplot portion may not be working right. See at
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu