I think the code you want to change is in CheckboxSetField.php in the function Field(). Sadly the existing formfields are all generated from the PHP rather then template files so it makes it a bit of a mission to change that 1 thing. Ideally all the html should be stripped out into templates. Hopefully we can make this happen if the form improvements for 2.4 go ahead.
Any reason why you need to change it? might be easier to just use CSS. (messy I know) but its that or you edit the CheckboxSetField field function (you could try and decorate the function)