Where to Stay? Choosing the right Hotel in/near San Francisco

FYI: hotels in San Francisco, Oakland, San Jose, many near SFO and others add to your final bill a Hotel Tax, officially a "transient occupancy tax." If budgeting closely, you may want to ask about this before booking your reservation.

Some visitors planning longer stays have found AirBnB and similar services offering houses, condos, and apartments for short-term rental a satisfying option. Realize, however, that with a rental, when you're looking for help--what's the best time to take a cable car ride? or is Alcatraz really sold out?--you are on your own.

"Downtown": Union Square, The Financial District & Nob Hill
Pros: easy access to all major transit corridors and taxis/Lyft,Uber; amenities associated with
  historic "grande dame" and boutique  hotels; many high-end restaurants and fast-food
  outlets, and luxury stores like Armani and Dior; walking distance from the Moscone Convention
  Center; proximity to the Theater District. If you want to catch a nap during the day or a
  concert/show after dark, this area is probably optimal.
  Cf. StayPineapple, Petite Auberge, The Marker, Chancellor, Marines' Memorial, Emblem,
  Westin  St. Francis, Fairmont, Mark Hopkins, Stanford Court
Cons: definitely "downtown" with crowds and panhandlers (usually harmless); Nob Hill is a steep
  climb from Union Square shopping but offers the magnificent Grace Cathedral (Episcopal),
  and panoramic vistas.
  
Northern Waterfront (Fisherman's Wharf, Ghirardelli Square)
Pros: proximity to sea lion colony at Pier 39 and The Exploratorium (world-class science museum
  oriented towards children and young adults), Ferry Building's excellent farmers' market; views of
  Alcatraz & Golden Gate & Bay Bridges; information for and starting point of many activities
  popular with visitors--rentals of GoCars, bicycles, Segway tours, big-bus tours, etc.; Boudin's
  Bakery (home of sourdough bread); the unique Musee Mechanique; lots! of souvenir shops; many
  seafood restaurants
Cons: farther from BART (interurban transit), Golden Gate Park, most residential neighborhoods;
  very "touristy" and crowded on holidays and during high season...children will often enjoy the
​  un-usual sights (like human "statues"), adults less so

SFO (Airport)
Pros: often less expensive, with most immediate access after a long flight
Cons: if intending to sightsee during the day or enjoy SF nightlife, requires finding taxis, Lyft/Uber
  or BART for half-hour to 40 min ride into and back out of downtown SF

on Lombard Street (b/w Van Ness and The Presidio)
Pros: less expensive motels; nice neighborhoods for walks nearby, especially the historic Presidio
  (a forested park): easy access to the Walt Disney Family Museum; walking distance to many!
  excellent restaurants on Chestnut & Union Streets
Cons: heavy traffic during rush-hours; parking hard to find and often expensive; minimal
  ambience
Cf. brand-new Lodge at The Presidio,
  also Inn at The Presidio (quiet, $$$ run by the National Park Service) 

Neighborhoods away from Downtown
(Pacific Heights, Cow Hollow, The Haight, The Castro, Japantown)
Pros: much more contact with locals and neighborhood gems: some hotels (e.g. Drisco) and B&Bs
  (e.g. Union Street Inn) have unique charm
Cons: will require time to travel on local transit/Lyft et. al. to the more popular attractions

SOMA (South Of Market Area)
Pros: close to Moscone Convention Center, MOMA (spectacular and unique Museum of Modern
  Art), Westfield Mall (Nordstrom, Bloomingdale's); 20-minute walk to Giants' stadium
Cons: 1-3 long blocks' walk to Union Square shopping

Oakland, Berkeley & Emeryville (east, other side of the Bay)
Pros: less expensive, quieter (other than Big Game and graduation weekends); flights into OAK
  often cheaper than into SFO; near some of region's best restaurants; closer access to Napa Valley
  wineries
Cons: requires using BART (interurban transit) or AC buses to reach San Francisco attractions
  which can add 40 minutes or more to your travel time each way

Sausalito (north, directly across the Bay)
Pros: quiet; shuttle to Muir Woods (check which days); panoramic views from some venues;
  near Cavallo Point (former military base now upscale resort run by the National Park Service)
Cons: bus and ferry access to The City may be challenging during busiest weekends for tourism

Silicon Valley (Palo Alto, Sunnyvale, Mountain View, San Jose...30-45 miles south, on The Peninsula)
Pros: if a taxi ride from Caltrain, then easy though distant access to San Francisco...Levi's Stadium
  relatively close
Cons: if far from Caltrain, requires rental car or long VTA or SamTrans rides to reach most places
  of​ interest