What’s the best way to synchronize times to millisecond accuracy AND precision between machines?

Just run the standard NTP daemon.

It does have options to take input from several GPS devices as well as talking to network servers.

Edit: I was referring to http://www.ntp.org/, not the one that comes with Windows.

I don’t have any suggestion as to what NTP clients are best for windows, but for Unix machines there’s no real reason to not run NTP.