[SalesForce] new window in visual force page

1) I do not see jquery being loaded in your vf page include the below line

<apex:includeScript value="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"/>

2) If you want to open link in a different window all you need to look for all a tags and set attribute to blank (

NOTE: You can adjust the href that needs to be redirected based on your need, I have set the code to redirect all hrefs to a new window.

<script >
$j = jQuery.noConflict();
$j(document).ready(function() {
$j('a').attr("target","_blank");
});
</script > 

When performing a Visualforce action (commandButton, commandLink, etc.), a POST request is performed to Salesforce and your page state is updated. This POST request removes the original query parameters from the URL. What you will need to do is to capture that query parameter in your Apex controller using ApexPages.currentPage().getParameters().get('cn') and save it in an Apex variable. The apex variable is then preserved and can be accessed in your Visualforce page.

You may also find it easier to use a PageReference method to load the print view once you have the case number in Apex, but if you choose to stick with javascript you can still use Visualforce merge fields in javascript, i.e. var myVar = '{!myApexVar}';