I can't speak for LIRR but Metro North spells out what type of boots must be worn. Some of the spec's include "a defined heel", "slip-resistant soles" and "At least a six-inch high ankle".
As far as uniforms, the only personnel required to wear uniforms are those that directly interact with the passengers. These include conductors, ticket sellers, ushers, customer service rep's and commissary personnel (bartenders).