I lived in that area (called 'Outer Sunset') for a year, I drove this route (next to SJ airport) to SF almost daily. enternalSun hit it on the head getting to brotherhood (see below)... The only thing about this area of SF is that it is virtually ALWAYS FOGGY (bring a jacket).

Get to the Boat House from San Jose Airport:

1: Take 880 South: You have to 'drive around' the airport to get to this onramp.

2: Take 280 North (San Francisco) Exit</b> Stay in the second lane from the right. after stevens creek blvd get over and you'll come to a fork immediately that is badly marked, take the right fork for north, left fork is south but that is not obvious. Stay on 280 untill you get into the city. stay in the left lane the entire way and you can ignore signs the highway automaticaly lets you off onto 19th. Note: This is my personal favorite drive (especially during twilight/sunset) and it takes about 30 min driving fast without traffic.

3: Exit BROTHERHOOD WAY. When you see the 40mph ahead sign, get over to the far right line quickly i think the junipero serra blvd exit comes fast and quick and it's round and circular. You'll see various chuches, temples, etc on your right (hence the name). It will dead-end into Late Merced Blvd. (your almost there!)

4: LEFT onto LAKE MERCED BLVD. (easy)
5: SLIGHT RIGHT onto JOHN MUIR DR.
6: Stay straight to go onto SKYLINE BLVD.
7: Turn RIGHT onto HARDING RD.

Lake Merced is actually a couple of lakes and a golf course. Harding rd drives between the two lakes and ends at the golf course club house (i think). I imagine there will be a bunch of tight ass cars in one of these lots listening to loud music (i think the boat house is in the middle of the parking lots) <see attached MapQuest arial photo>