Keep JS script

I use your google pagespeed tools that move all the JS into the footer. I do however want to keep the Google Analytics JS in the header. Is there any way of doing this?

Yes you can fix JS script and plugin will not move it.
https://www.foxnetsoft.com/documentation-noppagespeedtools

If you need to fix JavaScript code on selected place into the HTML page, you should use data attribute data-fixedscript="1" for it.

Example

<script data-fixedscript="1">/*body of script*/</script>
<script data-fixedscript="1" src="/Scripts/jquery-1.10.2.min.js" type="text/javascript"></script>