E-bikes would be a great way to get around the Embarcadero and northern part of the city (Fisherman's Wharf, Crissy Field and the Golden Gate Bridge) since you would be mostly separated from traffic on sidewalks and bike paths. If you want to ride across the bridge on the weekend you should actually ride the ferry TO Sausalito to save time and because it's a gorgeous trip, then ride back to SF FROM Sausalito. The reverse route can be much more crowded with rental bikes on weekends, which is why I recommend this direction. I would skip eating at Greens, there are much better places either in the Marina District or in Sausalito, depending on where you end up and your timing.
I wouldn't recommend riding in other parts of the city for novice bike riders, but if you have urban cycling experience you should be fine riding down to Golden Gate Park to explore. GGP is closed to cars on Sunday, which is nice if you're on a bike.
FYI the CA Academy of Sciences (CAS) is no longer located near SFMOMA, it's in GGP while SFMOMA is south of Market (SOMA). Both areas have lots to see, as mentioned GGP has CAS, the DeYoung Art Museum (maybe that's what cchrissyy was thinking of), the Japanese Tea Garden, Conservatory of Flowers, paddleboats at Stowe Lake, lots to do. SOMA has all kinds of cool museums like SFMOMA, African Diaspora, Contemporary Jewish Museum, and is close to Union Square/Powell St. cable car and the Embarcadero/Ferry Building so you also easily visit those spots.
Since the weather in SF is so unpredictable, if you don't do anything that requires reservations like going to Alcatraz, you may want to play it by ear and decide your itinerary when you arrive...if the weather is nice do something outdoorsy, but if it's blowing snot and freezing cold in SF (which may be the total opposite of the weather in Oakland!), do something indoors.