Take the Blue/Gold Line (think thats the name) ferry to Alcatraz and take a tour. That would certainly be a good 'cover' for the proposal. "I am a prisoner of your love .. will you ... "
Seriously, several of the upscale hotels have wonderful views on the top floor. The more expensive the better they would be able to work ahead of time with you on a surprise ring delivery. No specific suggestions .. OR something overlooking the Ocean like the Cliff House restaurant.
All depends on finances for this proposal! I would be you could hire a Mime from Pier 39 .. to follow her around for a while and then 'assist' with the proposal.
Best wishes!