Just thought I'd throw some advice out there for anyone wanting to buy canon gear in Tokyo. I have the full info on my blog and it seems to get a lot of traffic, so people are trying to get the good deals I guess.
Anyway, the two places most people will go when they are new here or just traveling through are the Yodobashi Camera and Bic camera chains. Both are actually pretty good, they offer 10-18% of the price towards points you can use towards other in store purchases, in the past I got a new 5D and had enough points to get a battery grip for free. These stores are a good option when something is about to be replaced, the price drops and the points get higher. Each store usually gives 1-2 years warranty as well which can be extended up to 5 years (although you end up using all your points for that, but it's peace of mind). These stores are all over Tokyo, the best Yodobashi is at Akihabara station, they have a massive selection there, every lens, body and strobe, you can try most of them out as well. For Bic, try the Yurakucho store (one stop from Tokyo station), again every item is there, a lot of it is on display and you can play with them. I do advise checking the online store price as well, sometimes it is cheaper and if you quote that in store they will drop prices.
However, for the cheapest and still very reliable places for new and second hand gear are Fujiyacamera in Nakano and MAP camera in Shinjuku. 90% of the time you will get a cheaper deal at these two stores, I bought my 5DmkII in Fujiya for 230'000 yen when it was 285'000 yen (plus 10% points at 28500 yen) in Bic which was a massive saving. Only 1 year warranty, but a huge saving.
For second hand gear you can get really good deals too. Each second hand item is rated in terms of quality and any fault is clearly pointed out. A lot of the gear has only been used once or twice and is in top condition, so maybe 90% of the new price, something with more wear and tear can be from 50-75% new price.
Fujiya is very popular and they sell out quickly, when I was after a 7D for a backup I was looking at second hand bodies, 14 were on display when I started looking, 10 minutes later when I made my purchase 10 had been sold. When I bought my 100mm f2.8L macro, I was going to get it in Fujiya second hand, there was one copy, I went to the ATM round the corner to withdraw the cash, came back to the store 2 mins later and it was sold. So, then I went to MAP in Shinjuku and got it. Slightly more pricey in map, only 2-5000 yen more for second hand/new gear, but they always have piles of everything second hand. They even have a whole floor of canon gear, just like heaven. They will have every canon lens second hand, I've already seen 8-15mm f4L fisheyes second hand and they just came out. My only problem with MAP is that sometimes the staff can be a bit off with foreigners. Most of the time you get someone really nice, but twice now I have had staff members refuse to show me an item, why I do not know. When I said I didn't need to inspect a new body once, I just wanted to buy it they refused to sell me it as it was "for display" and they refused to tell me when more would come in. Those were isolated incidents though, since then they have been OK.
Hope this helps.