What frame material are you interested in?
If you're interested in custom steel, a few builders that come to mind are Carl Strong, Dave Kirk, Richard Sachs, Vanilla, Independent Fabrications, Landshark, Curtlo, Heron, Rivendell, Pegoretti, Rock Lobster, Spectrum Cycle, the list goes on and on......
I'd recommend looking into a custom build sooner rather than later since some of these companies have long wait lists. For instance, I think the wait for a Vanilla is 22 months and for Sachs it's over five years.