Traverse City Pie Company: TCPC not only still makes all their magnificent Michigan cherry pies by hand, but its other pies are also pretty damned fine. If you don't live in close proximity to a great pie, a shipped TCPC pie is the way to go.
Julian Pie Company: Who know that the town of Julian, Ca. is mecca for West Coast apple pie lovers? These guys also ship, and if their pies are not quite up to TCPC standards, they're a close second.