In every station in Tokyo (and most of big stations in Japan), there are rental lockers available.
It's called "Coin Locker." They are really convenient & cheap.
You don't have to drag a luggage with you all day, you can just drop it at the station and do what you need to do.
The only thing is you will have to take your stuff out before the station closes – or you'll have to pick it up on the next day.
Unlike subways system in New York City or other big cities in the world, Japanese trains (including subways) do not run for 24hours.
*In Tokyo, most of them stop around midnight.
To check available trains for your location & schedule, try these:
(If you read Japanese, this one below is even easier to use)
If you have a smartphone (like iPhone), use an application designed to check the train schedule.
It's the best (Even better than the websites above)!!
Tokyo Photo Japan