I have lived in the Bay Area my whole life, lived in San Francisco for 2 years, now live in Sonoma and work in Napa. I would be happy to recommend some places to visit.
I guess it all depends on what kind of Honeymoon you want? The Napa Valley would be so romantic, lots of things to do, but not as busy as San Francisco. San Francisco would have a lot of activities to fill up your trip, many of which can be cheap or even FREE!
Places to stay in Napa:
The Carneros Inn is beautiful, and I think it would be SO romantic to stay in one of their Cottages. They are adorable! This would be a nice relaxing upscale place to stay, though it is set right outside of town (about 5 minutes from downtown napa). However, it is among the vineyards/beautiful views.
There is also The Napa River Inn that is nestled downtown overlooking the River, among shops, bakery, restaurants, etc. This hotel has old world charm & a beautiful garden & courtyard to walk through up to the river front that would be SO romantic at night.
There is also the River Terrace Inn, and several B&B’s in Historic Victorian Houses (cedar gables inn, The Beazley House etc.)
There are many fun things to do in Napa for a Honeymoon: Hot Air Ballooning, The Wine Train, shows at the Opera House, The Uptown Theatre, Hike up to Atlas Peak, movies at Cinemark, rent a car and explore St. Helena/Calistoga, check out the town of Sonoma.
There are many wonderful places to eat some of the best food in the world. LOVE Morimotos, Angele, Napkins…My favorite restaurants are in Sonoma: Saddles Steakhouse, The Girl and The Fig, and El Dorado Kitchen.
San Francisco has amazing places to stay:
Hotel Vitale-waterfront hotel, very grand. The Argonot Hotel is also waterfront/historic building. There is also the Inn at the Presidio which is a great hiking area & close to the Golden Gate Bridge. You really can’t go wrong with Hyatt Fisherman’s Wharf (quick connect to ferry, pier 39 etc.).
San Francisco has countless options for food, shopping, sight seeing etc. My personal favorites The San Franciscan Crab Restaurant, Greens Restaurant, Ruths Chris Steak house, the cheesecake factory above Macy’s (the view from the terrace is ridic)…
There is SO much to do in SF, blows my mind. You could walk the GG Bridge, take a trip to Alcatraz, walk on the beach, go shopping, go to the top of telegraph hill & see a view that will change your life…
I hope this helps, if you have any more specific questions let me know. Both great, though different choices for a Honeymoon!