Hi there!
There are a couple of good 1 day itineraries that you can find online, but as you'll be staying near Shinjuku I'm assuming you'll have visited the area around there the first day (Shibuya, Shinjuku, Harajuku, Meiji jingu). If this is the case then I recommend a plan where you do a bit of travel in the morning, and then work your way back to Tokyo station:
- Take suitcases and luggage to Tokyo station. Deposit cases in coin lockers for 1 day.
- Travel to Asakusa and take a look around the temples and then on to Kappabashi.
- From here take a look into Akihabara.
- Visit the top of the new Tokyo Sky Tree - the tallest tower in the world.
After this, it really depends on the amount of time you have left. If you've not seen the area around Shinjuku you could travel across tokyo and go see that, or you could head down to Ginza which is near the station and have a look around the great shopping streets there, or head over to Roppongi Hills for a look there.
If you don't mind getting up early, I also really recommend a trip to Tsukiji fish market before breakfast (I really mean 4am-5am levels of early!)
Hope this helps!