I haven't used Bootstrap, but as far as I know it's jQuery based. I.e., you can only use it in ePub3 books, and, AFAIK, pretty much the only major eInk device manufacturer that supports ePub3 is Rakuten Kobo Inc.
If you're wondering how to properly embed JavaScript libraries without getting epubcheck errors, check out my very simple jQuery based
epub3 test file.
Note that the test file won't work with Sigil, you'll have to open it with ADE 4.5 or other epub3 apps.