Generally speaking, the stations with Shin- prefix are the Shinkansen stations for that city when they can't build the tracks to the main station. For example, Shin-Yokohama, Shin-Osaka, Shin-Kobe, etc.

There are also stations that are built to connect to other train lines that don't reach the existing stations, i.e. Shin-Kawasaki, Shin-Imamiya, etc. Or rarely it may be a station built by different rail operator, such as Shin-Ochanomizu.