Kinokuniya in Shinjuku seems to have the biggest range. Book First in Shibuya is good too. After a while I start to think that the range of English books in those places is the norm. Then I go home or to another English speaking country and get overwhelmed by the choice :) Oh and I use amazon as well - but not so much for novels - unless its by an author who is consistently good. That instore browsing experience weeds out a lot of crap - and amazon reviews aren't particularly reliable I find.
thanks for the comments. i actually work at random walk in roppongi and we've started selling quite a few paperbacks for pretty cheap (mostly 500yen). i just wanted to know where my competition was as we ve recently decided looking to appeal more to foreigners. Before we were just appealing to japanese and that was stupid considering that we re in the heart of roppongi!
If you mean secondhand bookstores of foreign books in Tokyo, I recommend "Good Day Book" near from the Ebisu station.
http://www.gooddaybooks.com/contents/home/index_html?language=english