Point Reyes, Point Bonita and Muir Woods can pretty well kill off a day all by themselves. From the Fisherman's Wharf area I would plan on 2 hours to get to Reyes. 1.5 - 2 hours there, then at least 90 minutes (or more) to Point Bonita. Lots of scenery along the way. The road to Reyes and then the coast road to or from Bonita is really a driver's road if you like the challenge. For the passengers, it really sucks. You may well want to stop at various points to enjoy the scenery. If there is other traffic, especially locals, you may well be tailgated but don't let them push you to overdrive. Not very difficult to get into trouble on those roads.
This is a drive you have to experience to fully understand what you have been told. Both Reyes and Bonita are what I refer to as "destination lights". The lights themselves aren't really spectacular, but the trip to them and the view is off the scale.
If you read the stories I linked to, the road to view East Brother is a very poor one unless they have fixed it. Incredibly rough and narrow, with a lot of people trying to drive it way too fast. The best view of East Brother is from the top of the hills, about half way. Not a lot of places to pull over or turn around, so if you miss that spot on the way up you may well have to go all the way to the end of that road, turn around and catch it on the way back. It is, to say the least, a crappy ride.
If you go to
Quinn\'s Lighthouse Restaurant (the old Oakland Harbor Light), it is a little ways from the lightship. It has been a bit, but I would guess a mile or more (and I don't know that you would want to walk it.....) Dennis mentioned the burgers. They are most excellent - do be sure you don't accidentally order the large one because you will be able to feed most of the family with it.