The following is assuming that html files are generated from rmarkdown (.rmd) files. Rendering html from rmarkdown uses the rmarkdown package.
Remove CSS
Setting theme to null in header (front matter) of rmarkdown file per the documentation should remove the bootstrap css. Alternatively, you can specify your own css to be included if you like.
---
title: "Lorem Ipsum"
output:
html_document:
theme: null
---
Changing the tags: Use a different pandoc template.
If just removing the css was insufficient, you should be able to change the html tags to whatever suits you by creating your own pandoc template. You can change the template used by pandoc as per documentation
---
output:
html_document:
template: template.html
---
Looking at the call made to pandoc to produce the html, you can see that the template used comes from the rmarkdown package. It might be worth using that as a starting point for constructing your own custom template.
--template /YOUR/RLIBSPATH/rmarkdown/rmd/h/default.html
Keep the intermediate markdown
It might be useful to keep the intermediate markdown file when working on your own pandoc template. You can keep the markdown generated to be passed to pandoc by setting the keep_md in the header (front matter) of your rmarkdown.
---
title: "Something fascinating"
output:
html_document:
keep_md: TRUE
---
Hope this was helpful.