The Rail-Go Service at Tokyo Station will hold your bag for 420 yen per day (840 yen per day from the 6th day) up to 15 days. It's not clear if there is any size restriction.
http://www.tokyostationcity.com/en/i...on/locker.html
(Scroll down the page)
P.S. I found a Japanese language Q&A website which says the maximum size (L+W+H) is 200cm and 30kg so any bag which can be checked as a regular-sized bag on a plane should be ok.
Sorry, but where on the page is the "Rail-Go Service" noted? Is it under "Baggage Storage B1, inside Gransta Tokyo" subheading under "Coin Lockers/Baggage Storage/Same-day baggage hotel delivery service at Tokyo Station"? Thank you!