The stores you mentioned are actually good, and so is Onoden, Edion (and other electronics shop in Akiba), BIC Camera and Yamada Denki, but I think the right question to ask is "when is the best time to buy a good DSLR camera?" Because there is a season that all the models of the previous year would be in great sale. I got my Canon Kiss X50 for only 39,999 yen from its original 60,000 plus yen almost 4 years ago, and I am still using it this time. It's around January or February, during the clearance sale.
When you know the model. Go to a store, ask for a price (get a quote without tax if you are on a tourist visa), go to the next store, do the same and tell the price from the previous store. Repeat until you are happy and you can even go back to the first to tell him what you got, then get the best price. You will pay more if you stick to the price on the tablet. Work best in place like Akihabara with high density of camara sellers.