Hi there,
The 2 shinkansen terminals in Tokyo are at "Tokyo" and "Shinagawa" stations. There is no shinkansen terminal at Shinjuku station.
Tokyo station is the main shinkansen terminal, and connects the Tōkaidō (Osaka), Tōhoku (Shin-Aomori), Jōetsu(Niigata) and Nagano Shinkansen bullet train lines. The Hikari and Kodama bullet trains run on the Tōkaidō line from here. The Asama bullet train runs on the Nagano shinkansen line and also departs from here.
Shinagawa station connects to the Tōkaidō shinkansen, and is a stop before Tokyo station.
Hope this helps!