If you have never been to Glacier Bay, it is an experience not to be missed. So, if you are picking one or the other, I would choose Glacier Bay. As others have said, Mendenhall Glacier is different. If there is no other excursion in Juneau that you want to do, I would visit Mendenhall. You could wait until you get to Juneau to decide as there are local busses that will take you there.
Personally, I like the Hubbard Glacier the best so if you ever get a chance to see it, do so.