C.C.
Hi!
1) Take the Muni bus. It's probably half an hour. Details here: http://tripplanner.transit.511.org/mtc/XSLT_TRIP_REQUEST2...
2) See the trip planner above, but from the hotel to the pier, not that long. 20 minute walk. The ferry to Alcatraz is pretty quick, too. It's not a long distance - less than a mile into the bay.
3) Oh man. There's a LOT to do in SF. Museums - SFMOMA, the DeYoung, Exploratorium (it's for kids, but it's a blast for adults, too), the Museum of Natural History, the Conservatory in GG Park. Food - go out on a limb and try the House of Nanking (not that far from your hotel). It doesn't look like much from the street, but tell them you're adventurous, you're hungry, and what your budget is, and they'll blow you away with the best Chinese food you've ever had. If you want some finer dining, there are almost endless choices. You can't go wrong at Lulu (my husband and I got engaged there - it's homey, fun, and country french), Boulevard, Chez Panisse (it's in Berkeley, but WELL worth the trip across the Bay - take Bart to get there), Fifth Floor, Foreign Cinema (quirky, always a good time), Scoma (get the Cioppino - I promise it is the best you've ever had in your life). Honestly, it's hard to go wrong with SF restaurants. For Sunday brunch, you can't beat the Sheraton Palace on Market St. Skip the "view" restaurants. None of the truly great restaurants in SF have a view to match. :) Oh! Before your trip to Alcatraz, if you want lunch, since you'll be in the Ferry Building anyway, go to the Cowgirl Creamery's booth. They make a grilled cheese that will knock your socks off. And honestly, just a plain old glass of milk there is pretty awesome, too.
And as long as you're staying on the wharf, go ahead and take the cable car to Union Square. It's fun, and you can't do it anywhere else!