I spent the last few weeks contributing vertical writing support to the Calibre eBook reader, and it’s been merged into and released in the latest beta version. If you happen to have any vertically-typeset Japanese ePubs, you should be able to use it to read them.
If you run into any serious issues reading in vertical mode, please feel free to let me know. If I have enough time, I can try to fix them.
The biggest known issue is that furigana are sometimes cut off at the edges of the pages. If you’re a CSS wizard and have any ideas about how to fix this, let me know!