The
best font for a book depends on the book, there's no one-size-fits-all.
For LCD screens, Microsoft have spent a lot of work optimising their 'C' family to provide maximum clarity, but these are based on the use of ClearType, so won't work as well on eInk. In general you simply want a font with a reasonably large x-height and open apertures, and without too much stroke modulation. Personally, I really like Minion, and installed it as the general-purpose font on my reader.
The issue of text (or 'old-style') figures is a bit of a problem on ereaders. There's no standard unicode location for them, so fonts that do have them put the glyphs in one of the private areas and provide OpenType pointers that can be used by the more sophisticated layout programs. If you want to use text figures you can either use a font-manipulation program to paste the text-figure glyphs over the normal lining-figure ones (old Postscript Type 1 fonts used to come in an 'old-style' version where this had been done for you) or you would need to find out the private-area codes for the numbers and specify them as entities (&#[char code]
in the xhtml.