In case it's of any use to anyone else doing this trip, we walked from the Union Sq area to Sausalito a few years ago and got the ferry back.

A really nice day as long as you like walking, although there are some significant lengths of road between the GG bridge and Sausalito which lack sidewalks (or pavements, as we say in the UK). This typical lack of consideration for pedestrians makes the trip less enjoyable: it's not actually dangerous as long as you keep your wits about you, but you'll be sharing the edge of the road with broken glass and shredded tyres, and I guess these are also obstacles for cyclists.

Anyway, Sausalito's lovely and is pleasant for walkers and cyclists alike.