Here's an ekiben shop at the top of the escalator to platform 11 opposite the South exit of Shinjuku Station.



They also have smaller kiosks selling bento, sandwiches and drinks on most platforms - this one on the platform for the Chuo Line commuter trains. As others have said you don't see people eating bento on commuter trains.



And here's an ekiben site (in Japanese but you can use the translate feature in Chrome) where you can search for ekiben by the type of food, region/station and price.