The easiest way to get round the slightly odd build environment for NaCl is to just use TweetNaCl (http://tweetnacl.cr.yp.to/software.html) which just requires you to drop a single .c/.h file into your project - this isn't as performant as the reference code but in most cases this probably doesn't matter. The libsodium implementation seems overly complicated to me for most uses.
The NaCl API is reasonably simple and is fairly easy to wrap (plug - if anyone is looking for an example have a look at jim-nacl [1] which embeds into Jim TCL)
Might also want to checkout libsodium (https://github.com/jedisct1/libsodium).