Allow about 6 hours if you plan to do this combination tour. Be prepared for foggy, misty, cold weather and wind -- especially in June, July and August (sounds counter-intuitive but trust me). Wear comfortable walking shoes as Alcatraz requires a good walk uphill and also on uneven surfaces. Your tour circuit will be: Pier 33 to Alcatraz, Alcatraz to Angel Island, and then Angel Island back to Pier 33. BE ON TIME AND DO NOT MISS YOUR BOAT.
You will depart from Pier 33. Parking at the pier can be a bit scarce, but there are plenty of parking garages in the area. The combination tour begins with the ferry to Alcatraz. Once on Alcatraz I suggest skipping the welcoming announcements and beginning your trek uphill to start the tour. When you reach the top you will be given a headset in your language of preference. The tour itself is self-paced. You can stop your audio recording at any time to linger in a place of personal interest and hit 'play' when you're ready to move on.
When you get to the part of the tour about 'the yard' I suggest pausing and going through the door, down the steep steps and walking across the courtyard to a small doorway that looks like it's closed. You will see an incredible view of the Golden Gate and also of flowers. Most people don't know to do this. Don't be afraid to go off the grid and explore. NO FOOD IS AVAILABLE ON ALCATRAZ.
The ferry will then take you to Angel Island. It's about this time you will start to get hungry. Once you arrive on Angel Island you will be quickly shuttled and seated on a narrated, one-hour tram ride. Again, be prepared for wind and fog -- especially in summer. Angel Island has a history as a military post and is also known as the Ellis Island of the West for immigrants entering from the Pacific Rim. There is also hiking, camping, etc., on the island but you will need a separate itinerary if you want to linger to enjoy such activities.
After the tram ride tour you will have about 3/4 of an hour or so to visit the cafe before the ferry departs back to SF. The cafe food is mediocre at best and overpriced. You will be famished at this point and would eat dirty socks AND over pay for it - and believe me, they know it as the cafe employees are used to dazed, cold, and hungry tourists.
Bottom line: Dress for cold, fog and wind. Wear comfortable shoes -- it's not a fashion show. Bring your own sandwich, snacks and water so you are not held hostage by crappy, overpriced food on Angel Island.