Does the TOC appear when you export to ePub from InDesign CS6?
Have you tried validating the resulting ePub: http://validator.idpf.org
How are you creating the MOBI file, are you using the InDesign to Kindle plugin?
Is it the navigational or HTML TOC that's not appearing?
Kindle requires a separate html file for toc and same should be referenced in guide element in content.opf. In your InDesign CS6/CC document, generate table of contents on a page and make sure the option "Make text anchor in source paragraph" is checked.
Now export the file to EPUB 3. Open EPUB in Sigil (It is a free EPUB editor from Google). Goto Tools menu->Table of contents->Generate HTML Table of Content. This will create a new xhtml file and automatically add guide element in content.opf like this:
<reference href="Text/Untitled-21.xhtml" title="Table Of Contents" type="toc" />
Save EPUB and directly open in Kindle Previewer. TOC option should be enabled now and should be working.
Please try it out and let me know if it works.