Dunno what part of Tokyo you are staying in (probably inner metropolis I'm thinking), but the Book-Off in Nagayama is where I saw the most Eurobeat at. I'm not sure if you're looking for older stuff or like SEB200+ though. Book-Off has mainly older stuff though like before 2000. It's kind of hard to find things that come out after 2000 in Book-Off. Be sure to check out ALL of the sections. J-pop, Yougaku (洋楽), 500 yen, and 250 yen. Also, they are sometimes tricky and have sections called クラブ/ダンス at the end of the alphabet in the 250/500 yen sections. Check out オムニバス (Various Artists) as well.
Only problem is, Nagayama is a little far from Shinjuku area but I dunno where you're staying. Also, it's very difficult to walk to it from Nagayama Station (永山駅). You have to take the bus probably. I've never taken the bus at Nagayama though (didn't have time). Found some info online though.
Book Off Tama Nagayama (6-29 Nagayama, Tama-shi 206_0025; Free shuttle bus
departs from Keio-Odakyu Nagayama Station. 2 runs per hour on
weekdays, 3 on weekends. Go down stairs on the left side of coffee
shop and wait at the island beyond the taxi pool. About 10 minutes
to Book Off. The additional weekend shuttle runs stop by at Tama
Center Station. 357-2701) "Very large used bookstore. Quite large
foreign section: 4 high shelves. Also sells videos, audio CDs,
video games and toys." Open 10-22. [08/11]
(taken from
http://www.leepers.us/evelyn/bookshops/jp-yhama.htm)
http://www.bookoff.co.jp/shop/shop71002.html At the bottom it says the shuttle stops at 20:20.
[電車:
京王相模原線・小田急相模原線「永山」駅から無料シャトルバスあり。
駅前ロータリー・タクシー乗り場脇から毎日運行。最終便は20:20永山駅発。永山駅からバス約10分。
※詳しいダイヤについてはインフォメーションをご確認ください。]
http://www.bookoff.co.jp/files/news/201 ... tlebus.pdf
good info about it. I wish I had known there was a shuttle from Tama-Center when I was there -_-
Where are you staying? You should maybe consider going to the para clubs even though they are mainly in Roppongi these days. How good is your Japanese?

I went to the Book-Off in Shibuya and it was kind of lame for Eurobeat... but yeah, check out as many Book-Offs as you can when you go to Japan.