We recommend flying into SFO and either ubering or renting a car to drive into the city. It's about 25 minutes without traffic. If you find a better flight into Oakland, that's about 40 minutes into SF without traffic — and there's also the option to take BART (public transit).
There is no shortage of lodging options, from the bigger chain hotels downtown, to smaller inns and AirBnBs dotted around the city. Since San Francisco is pretty small, anywhere you stay will likely be 20-25 minutes max to the venue (Log Cabin at the Presidio). Below are some recommendations that are closest to the Presidio and particularly charming.
The first two, Inn at the Presidio and Lodge at the Presidio are sister hotels near each other on the main square in the Presidio.