Have much to say about both W3TC and pagespeed, but will try to stay on the point.
You should never have a JS external element in you HTML as part of the actual content, they should be either in the head element (but only scripts that must be loaded before the page finishes loading) or just before the end of the body.
CSS should be only in the head element.
The assumption is that if you decided to violate those basic performance rules you probably had a very good reason for that, and no plugin with a sane author will try to rearrange it for you as you can easily break the page if things are not being loaded in the right order.
So you need to understand first why do you have JS and/or CSS at that part of the page, and if it is not needed then you need to change your code to move them to the header or footer. Caching plugins have totally nothing to do with it and should stay away from even offering page changing functionality like that.