not everything can be found in those 3 places...
i recommend magazines rather than books because information is newer, there are sometimes discount coupons in magazines, and the sources are easier to trace. information in books are often dodgy, with few statements to back up their logic. also, if you want a more local experience, buy local magazines like Tokyo Walker, Non-no, Hobby Japan, GoodsNavi, etc... (you can buy these at Sogo, but better and cheaper just to get them at the airport when you arrive. train from Narita to Tokyo city takes 1hr anyways, so lots of time to read). i've read lots of HK and Taiwanese magazines, and usually the places they suggest are... crowded with other tourists, and it will feel more like HK or Taiwan, with all the c9(obasan) bitching and gossiping, it really becomes irritating when you've payed thousands of dollars for a ticket to experience something different.