There are a bunch of packages (Aquarium of the Bay, AT&T Park tour), but none I've heard of that include those two.
http://sanfrancisco.ridetheducks.com/special-offers.aspx
These discounts may have expired. They say to show the ticket for the discount.
http://sanfrancisco.ridetheducks.com/special-offers/wacky-quackers.aspx
I did a little checking and found this:
http://reserve123.com/tours/alcatraz-ticket-duck-tour-san-francisco-after-march-11
I checked for April 29 (just picked a date) and it's $75. An online booking for Ride the Ducks is $31. The adult day tour to Alcatraz is $30 from the official website. The website for the package doesn't say if it includes transportation from the Ducks ride to Pier 33 (where the Alcatraz ferry boards).
You might be better off just booking directly. You would also have more flexibility to do this on separate days.