Why not let website visitors make your measurements by loading the JavaScript files from the CDNs in the background?

Something like (untested):

    var i = 0;
    var urls = [
      "http://cdn.jsdelivr.net/jquery/2.0.3/jquery-2.0.3.min.js",
      "http://code.jquery.com/jquery-2.0.3.min.js",
      ...
    ];

    function measureRemaining() {
        if(i >= urls.length) return;
        var url = urls[i++];
        measureLatency(url, function(latency) {
          // TODO: post (url,latency) to back-end
          measureRemaining();
        });
    }

    function measureLatency(url,responseFn) {
        var script = document.createElement("script");

        // Bust through browser cache
        script.src = url + "?bust=" + Math.random():
        
        var start = new Date().getTime();
    
        script.onload = function() {
            var end = new Date().getTime();
            var latency = end - start;
            responseFn(latency);
        };
    
        document.getElementsByTagName("head")[0].appendChild(script);
    }

    measureRemaining();

In this way, you'll get actual end-user performance from a (hopefully) large number of different network locations. You will probably want to do this in a separate iframe to avoid changing the behaviour of your webpage.

In the context of full web pages how I've seen this done is by embedding a Javascript call that occurs after the page is loaded to your site. I suspect you could do something similar with this resource.

Alternatively you can look at what CDNs are hosting the resources and then just use the existing tools to compare the expected performance of each CDN. Of course this comes with a few caveats:

1/ Performance may be different on a given CDN depending on which "package" the customer has purchased. I know was the case ~1-2 years ago for Akamai.

2/ A CDN may perform well for small objects but not for larger objects, make sure you look at representative benchmarks.

3/ JS CDNs using CDN load balancing services like Cedexis mean more work to find all the CDNs that are being load balanced across (jsDelivr uses Cedexis)

(edit: formatting)

One thing that would be interesting is "Latency from where". Yandex seems to do pretty badly, but is that also true if you're in Russia?

Nice point. We've been planning a map based visualization. That would definitely help in this regard.