Flight
The closest airport to fly into would be STS, Santa Rosa, but it can be pricey to fly into. SFO and OAK (where we mostly fly in and out of) is nearly the same time drive and flights are usually less expensive. SAC is also close enough if you rent a car and drive.
Travel Note
A few months after we had finalized our wedding date and venue, we found out there is a race at Sonoma Raceway the day after (June 23rd). This has made hotel prices go up. I would suggest booking a place ASAP. If you stay a bit out of town of Sonoma, I would suggest renting a car. Uber and Lift is also in the area! I think AirBnB or VRBO will be better options for price stability. Petaluma is only a 30 min drive and there are lots of hotel offers there, too.
House Or Rental
There are lots of house and apartment rental options through VRBO and AirBNB in Sonoma and Napa area. I would suggest being within a 5-10 min Uber from the Sonoma Square. https://www.vrbo.com/vacation-rentals/usa/california/sonoma/sonoma-plaza https://www.airbnb.com/Sonoma
Hotel
Not right on the Square, but a cute little place to stay.
Hotel
Romantic BnB type hotel on the square.
Hotel
Some of their rooms are more like condos and have a lot a room. You can fit multiple people in them! Also great pool on site.