Agree with above that it is dependent on career goals. Many more programs will allow adequate training to be a competent clinician (especially if goal is seeing almost all MS in private practice setting) than those that can foster a clinical or basic science career or provide enough exposure to be good at less common diseases in the "autoimmune neurology" realm.
Some programs to consider:
If you are interested in basic research, UCSF, MGB, Hopkins, Yale, Stanford, WashU, UPenn
If you are interested in clinical research, CCF, Mayo, Colorado, UTSW, Mt. Sinai, in addition to the above
Among the many other programs with strong reputations include OHSU, Utah (notably for autoimmune program), NYU, Duke, Columbia
There are several other good places out there and remember a lot depends on goals and situation