The data is based on Pingdom, yes. Recently we made sure each CDN is monitored from the same group of servers.

It's probably not ideal. It definitely would be great if we could provide some alternative metrics. Ideas are welcome. :)

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();

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)