Hi,
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:
<guide>
<reference href="Text/Untitled-21.xhtml" title="Table Of Contents" type="toc" />
</guide>
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.
Regards,
Pooja
InDesign Engineering