Hi,
As per my understanding , in your javascript first find the Usercontrol instance in your page and then find the text box in your usercontrol.
This is how i did in my aspx.cs.Should be the same in javascript as well.
i have a usercontrol in a tab panel in my aspx page.
UserControl ucname = new UserControl();
ucname = tabPnlUser.FindControl("User") as UserControl;
TextBox txtucFirstName = (TextBox)ucname.FindControl("txtFirstName");
txtucFirstName.Text = "";
Hope this helps.