I haven't yet been able to visit Malt-ya. It is just round the corner from Quercus and in fact the proprietor of Quercus, Mr Watanabe, used to work here before starting his own place. They do their own bottlings and, judging from Dr John Hawkins report, usually have at least a few bottles of Japanese whisky on offer.
Open 5pm to 5am, Monday to Saturday. Closes 2am on national holidays.
1-8-6 1F Dai2 Sasaki-biru
(I have an alternative address: 1-8-6, 1F DKY12 biru, Higashi-Ikebukuro 170-0013. Not sure which is correct but there is a sketch map on the website at the bottom of this page.)
Address in Japanese characters
170-0013, 豊島区東池袋1-8-6 第２佐々木ビル1F
Malt-ya on Nonjatta's map of Japanese whisky bars.