I agree with previous posters that biccamera and yodobashi are the
stores of choice. I have bought items from both. For the more
common items their prices are the same but the point amounts can
differ a bit. Both stores have online webfronts.
http://www.biccamera.com
and
http://www.yodobashi.com . You can search prices without knowing any
Japanese. For example if you are interested in Canon's 70-200mm
lenses put "EF70-200" in the search box minus the quotes. The price
should be the same but the point amounts in the online store will
be a bit higher (probably 3% more).
For the limited amount of time that you have I suggest sticking
with Yodobashi's main photography store in Shinjuku and Biccamera's
in Ikebukero. If you want to compare prices between the two
Biccamera also has a good photography store in Shinjuku in the
Odakyu department store. It is about five minutes walk from the
Yodobashi store.
Best Biccamera store for photography is in Ikebukero east side of
the station. Go out exit 35 from the north east corner of the
station. Keep going straight once you go out the exit until you
come to a big intersection. Look for the Lotteria fast food
restaurant. The store is next to it.
Best here means biggest range. If you want to play with lenses
before you make your final decision then Biccamera is better. In
Ikebukero they even have the EF600/f4 mounted on a head with a body
for customers to play with.
It is easy to get confused. Biccamera have four stores on the east
side of Ikebukero station (and one on the west)! You want the one
that basically has only camera gear. Also Yodobashi have two stores
very close to each other. Again you want the one that has basically
only camera gear.
I have gotten a point card and bought stuff from biccamera in the
same morning and also used the points on the card. Yes they want an
address but it isn't used for anything so just give them a hotel
address.
I strongly suggest doing your research using their websites as lens
prices are strange in Japan. For example the EF70-200 f/4 L and
EF70-300 IS are almost the same price in B&H but vastly different
prices in Japan. The EF70-200 f/4 is much more expensive in Japan.
But the EF24-105 f/4 L is a real bargain in Japan compared to the
US. I have no idea why.