これなら動いた

HtmlDocument doc = webBrowser1.Document;
if (doc == null) return;

HtmlElement jsElem = doc.CreateElement("SCRIPT");
jsElem.SetAttribute("language", @"JavaScript");
jsElem.SetAttribute("type", @"text/JavaScript");
jsElem.SetAttribute("src", "http://localhost/hoge.js");

if (doc.Body == null) return;
doc.Body.InsertAdjacentElement(HtmlElementInsertionOrientation.BeforeEnd, jsElem);