The problems in Yosemite concern sleeping in the "luxury tents" at Curry Village, deer faeces etc have become trapped between the double walls of the tents and caused potentially an enormous problem. I personally wouldn't allow this to prevent me from visiting a wonderful place.
If you want to visit Alcatraz, book a day or two before you want to go, it's almost impossible to buy tickets on the day.
Check if you'll be there during Navy Week, the Blue Angels fly above the Bay, it's wonderful to watch, the city is heaving!