People eat bento only on intercity trains. All the major stations have bento stands, sometimes even on the platform. (At Tokyo and Ueno, as I recall, you can buy your bento after you enter the Shinkansen area but not after you enter the actual platform.)
Shinjuku has bento stands all over, and if you want a bite to eat before getting on the train, lots of snack stands, fast food, and a couple of arcades full of a variety of shops and restaurants, plus connections to department stores.

If you go to a bento stand, there will be samples behind a glass case with prices--they are ready-made, not made to order, so buying one takes no more time than buying a newspaper. Point to the type you want, and the counter attendant will get one off the shelf for you. If the attendant crosses his/her arms in an "x" shape, that's the Japanese gesture for "not possible, not available, no good."

The most popular kind is the makunouchi (ma-koo-no-oo-chee) bento, which has rice with a pickled plum (umeboshi) and a variety of small servings of vegetables and meat or fish, but there are many other kinds, and as Always Aisle noted, each major region has its own local bento. The containers are sometimes as distinctive as the food.

They usually come with a napkin, a pair of chopsticks, and sometimes a moistened hand wipe. Buy a separate beverage, and you're all set.

I'm not sure how early you will be departing, but the Shinkansen have vendors who walk through the train selling food and beverages, including green tea, coffee, and canned drinks, including beer.