How to remove the link tag from the head using javascript?

Well you could store all the links you create in an array and then iterate over them and remove them:

let bootstrapTheme = true;
let head = document.getElementsByTagName('head')[0],  
stylesheets = ['https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.bundle.min.js','https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js']
var links = [];
stylesheets.forEach(function(stylesheet) {
    var link = document.createElement('link');
    link.rel = 'stylesheet';
    link.type = 'text/css';
    link.href = stylesheet;
    head.appendChild(link);
    links.push(link);
});

if(!bootstrapTheme){
    links.forEach(function(link) {
        link.parentNode.removeChild(link);
    });
}

But if I were you, I would simply wrap the first .forEach() in the if and wouldn't add the links if not necessary:

let bootstrapTheme = true;
let head = document.getElementsByTagName('head')[0],  
stylesheets = ['https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.bundle.min.js','https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js']

if (bootstrapTheme) {
    stylesheets.forEach(function(stylesheet) {
        var link = document.createElement('link');
        link.rel = 'stylesheet';
        link.type = 'text/css';
        link.href = stylesheet;
        head.appendChild(link);
    });
}

I guess, this solution might be helpful:

// bootstrapTheme boolean:
let bootstrapTheme = true;
// Your links:
link_srcs = ["path/to/booststrap1", "link/to/bootstrap2"]
// Creating link tags:
link_srcs.forEach(src => {
        link = document.createElement('link');
        link.rel = 'stylesheet';
        link.type = 'text/css';
        link.href = src;
        // NOTE: instead of declaring head variable, use document.head
        document.head.appendChild(link);
    }
);

if (!bootstrapTheme) {
  //Getting the link tags and looping them:
  document.head.querySelectorAll("link").forEach(link => {
   // you can use link.remove() too, but this solution is more supported and polyfilled:
   if (link.src in link_srcs) link.parentNode.removeChild(link);
  })
}

and also there is better and shorter code too:

// bootstrapTheme boolean:
let bootstrapTheme = true;
// Your links:
link_srcs = ["path/to/booststrap1", "link/to/bootstrap2"]
// Creating link tags depending on the condition:
if (!bootstrapTheme) {
link_srcs.forEach(src => {
        link = document.createElement('link');
        link.rel = 'stylesheet';
        link.type = 'text/css';
        link.href = src;
        // NOTE: instead of declaring head variable, use document.head
        document.head.appendChild(link);
    }
);
}

I would do this the following way.

Step 1: List all link tags in an Array

Step 2: Remove all elements listed in the Array

var list = document.head.getElementsByTagName("link");

var num= list.length;

for ( var i =0; i<num; i = i++){

head.removeChild(list[i]);

}