As we all know, one can go to a well-reputed program w/excellent teaching and not learn a thing (by not paying attention/etc.), and someone else can go to a defunct program and become an expert (by working hard/etc.). Obviously, the most important factor is you - your motivation and plan/direction.
If you are interested in going into academic EMG/neuromuscular disease, it is often helpful to match residency at a program that may keep you on as their fellow. IMO, the stronger programs include:
Mayo, UCSF, Partners, Columbia, Penn, Hopkins, NIH, WashU, Cleveland Clinic, Case Western, Rochester, Baylor (at least a few years ago), Michigan, Utah, UAB, and Miami.
However, a lot of it is what you make of it (see: first paragraph) - right? Good luck on your match.