Developing WordPress Theme using CSS framework like Bootstrap

Neither,
In wordpress styles and scripts should be properly en-queued through your functions.php file rather than hard-coding them in your html.

The wordpress way of adding a new css file, be it bootstrap.css or any other is to use wp_enqueue_scripts hook.

The following code should be in your theme’s functions.php

/**
* Proper way to enqueue scripts and styles
*/
function wp_theme_name_scripts() {

    // enqueue your style.css
    wp_enqueue_style('style-name', get_stylesheet_uri() );

    // en-queue external style
    wp_enqueue_style( 'bootstrap', 'https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-beta.2/css/bootstrap.css' );

    // enqueue your script
    wp_enqueue_script( 'script-name', get_template_directory_uri() .'/js/theme_name.js', array(), '1.0.0', true );

    // Other styles and scripts
}
add_action( 'wp_enqueue_scripts', 'wp_theme_name_scripts' );

This is a great tutorial on how to load css the right way in wordpress.

Check out WordPress documentation for more info on enqueueing styles

Update:

Underscores Framework already has the function defined in the functions.php.
Open your themes function.php and find the function named yourTheme_scripts(), and add the following line to include the Bootstrap library.

wp_enqueue_style('bootstrap', 'https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-beta.2/css/bootstrap.css' );

Your function in the underscores’s file should look like this:

/**
* Enqueue scripts and styles.
*/
function yourTheme_scripts() {

    wp_enqueue_style( 'yourTheme-style', get_stylesheet_uri() );

    //Enqueue bootstrap css library
    wp_enqueue_style('bootstrap', 'https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-beta.2/css/bootstrap.css' );

    wp_enqueue_script( 'yourTheme-navigation', get_template_directory_uri() . '/js/navigation.js', array(), '20151215', true );

    wp_enqueue_script( 'yourTheme-skip-link-focus-fix', get_template_directory_uri() . '/js/skip-link-focus-fix.js', array(), '20151215', true );

   if ( is_singular() && comments_open() && get_option( 'thread_comments' ) ) {
       wp_enqueue_script( 'comment-reply' );
   }
}
add_action( 'wp_enqueue_scripts', 'yourTheme_scripts' );