With RStudio and knitr I see that I can add a TOC with the following code in my .rmd file.
----------------
output:
html_document:
toc: yes
---------
You can use JQuery to relocate the TOC to an arbitrary position in the file. Simply insert a heading where you want the TOC to go, and use the ID generated by rendering the R Markdown file. For example:
A heading called "Table of Contents" somewhere in the R Markdown file will receive id "table-of-contents". The TOC has id "TOC". The Jquery bit above selects that TOC, and inserts it after the "Table of contents" heading, wherever in the document it's located.