Haha.. listen to me...You won't regret. Next to Shinjuku, there a small residential district called Yoyogi, much more peaceful. You have time, drop by for a coffee. No need to take train, just walk over to Kinokuniya, go down the stairs and it's less than 100m away. Meiji Shrine is just 2 stations via JR line. Stop at Harjuku.
If you are planning a trip to Tsukiji fish outer market, and if you staying at Shinjuku, take the Oedo line and stop at Tsukijishinjo (and not Tsukiji station). Tsukiji market is near Ginza. From the outer market, take a nice walk to Ginza. If you are a smoker, please note that This is a non smoking street. If you really need to smoke, go to the backplanes of Ginza, but please don't litter. Bring your own portable ashtray.