A couple of things:
Make sure you take some jackets with you or at least some sweaters. It will be cooler than you think!
The CY and Marriott are wonderful at Fishermans Wharf for a family. However, I don't know what category they are.
My last visit was delightful as I stayed at a CY by Larkspur and took the ferry to Fishermans Wharf. It was fun and really a bargain compared to the prices in SF. You could walk to the CY across the street from the Ferry. It was a very peaceful place!
Jerry is being way to kind using the cooler than you think phrase. He really meant once the fog comes in and the sun is gone it will get COLD!
San Francisco is a wonderful place to visit, so many things to see and do, then you get to eat as well. A must is the Alcatraz Tour, sign up early as they fill up weeks in advance and make sure to sign up for the headsets as well.....a great experience not to be missed as well as North Beach dining, Chinatown, the Golden Gate Bridge and north the cities of Sausalito and Tiburon are quaint fun spots to take a ferry ride to each location.
Enjoy a fine trip and keep us updated on your findings for a hotel and trip.
Marriott and Courtyard Hotels near Fisherman's Warf are ideal for touring, especially on NW side of town (Alcatraz and ferry boats, Coit Tower, Golden Gate Bridge,Stinson Beach, Muir Woods, etc.), and are very close to BART cable cars (Powell Street - my two grandsons shown in photo below ) but parking is not free and hotels are Category 8 and 7.
I've stayed at Marriott and Courtyard, Fisherman's Warf and Courtyard on 2nd, but none of these are category 4-5, nor offer free parking. However, we parked on street near Fisherman's Warf and paid parking meter, but you'd better move your auto before 7 AM, or the street cleaners will make you wish you had! The hotels near Fisherman's Warf are most strategic ones for boat to Alcatraz, walks up famous, crooked street - Lombard Street - and Coit Tower, and close access to Persidio and museums, along with Powell St. cable car.
If you need a cat. 4 or 5, either the Courtyard or Residence Inn (I would opt for the Res. Inn) at Oyster Point are good options. Parking is free, and they're both right on the bay, with a nice trail right outside the hotel. The CalTrain station is only 1 mile away (free parking) and the BART station is only 2 miles away at the airport.
The hotels also have free shuttle service to the airport (and bart), the CalTrain station, and Union Square. BART will only take you to Market Street, so from there you will need to either walk or use the SF Muni transportation system, which is good. And of course you can always drive if you want to, but parking can be expensive. It does get cold at night. The Louis Vuitton Cup yacht races will be going on in the Bay while you are there.
I'm not sure you're going to find a category 4-5 hotel near BART and with free parking. It will depend on how far you want to stay from the city. I like staying in the East Bay, but close to BART is a must. Getting into the city is easy. Once there from anywhere along Market St, Muni will get you all over the city. Buy a 3-day pass for convenience. A good place to pick one up is a the visitors information center just outside the Powell St BART station. It's a good first stop and you'll be right next to the cable car turntable (always a good photo op).
The Marriotts in Oakland and Walnut Creek are close to BART, but you'll pay for parking. You might look at other East Bay properties, but you'll likely be driving to a BART station to get into town (which isn't really a big deal). From past experience, you really don't want to have a car in the city nor will you need it.
Good luck and have fun, but heed the warnings about how chilly it gets after the sun goes down.
Not even when when the sun goes down as much as when the fog blocks the sun and the wind is blowing in across the bay. A few times we've been walking back to the hotel after a mid day bite to eat and some wine with a warm sun on us only to find the temperature seem to fall 20 degrees with the fog rolling in.....brrrrrrr but still an awesome place all of it.
I have stayed at the Courtyard Larkspur Landing several times. It is a few minutes walk to the ferry that comes right into the wharf area of San Francisco. Parking is free. It is a Category 5 hotel and very peaceful. The ferry ride itself is pretty cool. Most visitors to San Francisco also want to visit Sausalito and Muir woods and Larkspur Landing is convenient to both. The wine country (Sanoma and Napa) are also much closer time wise to Larkspur.
Sorry, I can't help you with the hotel ( I have only stayed at, San Francisco Marriott Fishermans Wharf. ). I only wanted to mention a tour to take. My husband and I took the Alcatraz Tour at Night. (Alcatrazislandtickets.com) I would recommend this. The fog was rolling in while we were on Alcatraz island!! We were there in September and yes we had a jacket/sweater)
I agree with bejacob in that I prefer to stay in the East Bay and take BART into the city. The Renaissance ClubSport is a great hotel (category 5, up from 4) located about a block from the Pleasant Hill Bart station. As a platinum, I was upgraded to a nice suite and received full buffet breakfast for 2 for the week. This was prior to the 'enhanced' brand standards, so you may want to confirm that they are still offering the full buffet rather than just continental. There is a charge for valet parking, but we didn't have a car for most of the week because we didn't need it. We rented for 2 days at the local Hertz to drive to Napa (30-45 minutes). This hotel also provides free access to a world class Health Club onsite. I believe it is the nicest category 5 hotel in the bay area, much better than the Marriott and Courtyard in Fisherman's Wharf.
I don't know if it is convenient to the BART, but the San Mateo Marriott (a category 5 hotel) has a lot of suites so you have a good chance of getting upgraded even on a rewards stay. Parking is, I believe, $22/day, but they threw it in for free on a recent rewards stay I had there. The hotel is nice too and I enjoy it a lot more than the nearby Courtyard Oyster Point, which is also a Category 5 hotel. There are many category 4 Courtyards in the Bay Area--Palo Alto, San Mateo, Cupertino, etc.
I hope you enjoy wherever you stay.
My wife and I spent 4 nights in SF in mid-July, 2 nights at the JW at Union Square and 2 nights at the Westin St. Francis. we took BART from the airport and used Muni and walking to get everywhere. BART had been on a short strike in early July and then took a 30 breather. Before you make plans that involve using BART, you should check to make sure they are not going back on strike. I think that "free parking" is an oxymoron in downtown SF and that is why we planned on using Muni. Note, if you buy a multi day Muni pass it covers bus, trolly and cable cars, a heck of a deal.