eBook is usually considered a generic name for the various digital formats. If you mean ePub, then InDesign is a good tool for producing these, but you really need the latest version: CS5.5.
If by graphic novel, you mean single column text with the occasional inline illustrations or photographs, then that can be done with this application.
But producing ePubs is not intuative you'll need some training such as that produced by Lynda.com: http://www.lynda.com/InDesign-CS5-5-tutorials/to-EPUB-Kindle-and-iPad/82258-2.html?srchtrk =index%3A1%0Alinktypeid%3A2%0Aq%3Aindesign%20cs5.5%0Apage%3A1%0As%3Arelevance%0Asa%3Atrue% 0Aproducttypeid%3A2
and Video2Brain: http://www.video2brain.com/en/products-92.htm
An excellent book is "EPub Straight to the Point" by Elizabeth Castro
And, if you can afford it personal training, in the UK Certitec http://www.certitec.com/ provide this.
(I have no connections with the organsiations mentioned.)