The best book for Lua by a longshot is Roberto Ierusalimschy's _Programming in Lua_, second ed. (http://www.inf.puc-rio.br/~roberto/pil2/) It covers the core language and the C API with the same clear, erudite treatment as K&R. (He is one of the core Lua authors.)
Lua is transitioning from 5.1 to 5.2 right now, which introduces some changes (improvements to the GC, adding to the standard libraries, and improving the package/module system). The main language and C API haven't changed significantly from 5.1; you should be fine if you learn 5.1 now and update later. Lua is small enough that you could add 5.1 to your projects as a library dependency and maintain it yourself, though - it's only about 16,000 lines of code.