What is the best programming language for the job?

I'll second the advice above and tell you to let the programmer decide. Just make sure you're thorough in expressing what you want your application to do.

An ePub is essentially just a collection of img and xhtml files that have been zipped. You could do it without a specialized library at all, just creating the text elements, using file utilities to copy the image elements, and invoking a compression utility. I might still use the libraries anyway, though, depending on what you're doing, safer to use something that other people have proven to be reliable rather than build your own. Of course, this assumes that you want to use the ePub format, which has probably the lowest barrier to entry and is generally a good choice.

The best language for the job is often just the language you know best. If you're hiring someone, just go by whatever mainstream language they prefer.

Any of the modern "dynamic" style languages (like PHP, Ruby, and Python) would work fine and be easier/quicker than alternatives, especially if you either forgo a GUI, or do a web-based one. The most important questions to answer are a) what format(s) do you want to support, and b) is there a good library available in the given language to manipulate that format. For instance, here's one for working with EPUBs in PHP that seems well-regarded (on a cursory inspection): http://sourceforge.net/projects/oplsepublibrary/

My programming skills are rather limited, so I would probably end up hiring someone to code it for me. Then let them code it in whatever they want, or you're arbitrarily restricting your pool of available developers for no benefit.