Hi Penny
I would book Alcatraz for early afternoon on Day 2. There is an included sightseeing tour in the morning which you won't want to miss. This finishes late morning and is followed by an optional harbour cruise. So I would book for 1pm or later if you don't want to do the harbour cruise, or for 2pm or later if you want to do the cruise as well.
Kind regards,
Olly, your editor