Hi Christine
The best time to book Alcatraz is the early afternoon of day 2.
You will have an included city tour in the morning, which usually finishes around noon. Then there is an optional harbour cruise. If you want to book that, I would book Alcatraz for around 2pm. If you're not worried about the cruise, you could book Alcatraz any time from around 1pm.
Kind regards
Olly, your editor