A novelised version of 5cm was first serialised in the Da Vinci magazine between May and October 2007 (i.e. issues no. 157 - 162) which included a number of sketches in them. A hardback release was then made available on December 14th. It is considered a "light novel" in Japan due to the fact that it's short and is related to an Anime piece of work.
Unfortunately as far as I'm aware, it has not been officially translated into any other langauges including English at the moment so you will just have to bear with my fan translation at the moment. A Simplified Chinese fan translation is also available for those of you interested and an official Thai translation was released with the "Makoto Shinkai's Memory Box".
As you may have read from the introduction, Makoto Shinkai had brainstormed many ideas by writing a number of short stories before he picked three of them to produce 5cm. One of those ten draft stories that Shinkai wrote but never made it into the final production of 5cm was "The Sky Outside The Window" which anyone who either bought the limited edition DVD from Japan or the Taiwanese collector's edition had a chance to read.
Maybe you'll notice some similarities between Miyuki and the characters in the movie.
If you wish to get a copy of the Japanese novel, copies can be found on Yes-Asia or HMV Japan.