I am using FooTable v3.1.5. When I want the search box to appear I add the following markup...
<table id="mytable" class="table table-striped table-bordered footable" data-filtering="true">
if I wish to hide the search box i remove the attribute 'data-filtering'.
Example:
<table id="mytable" class="table table-striped table-bordered footable">
I then use JavaScript to initialize the table...
$(document).ready(function () {
$("#mytable").footable();
});