I will be travelling to SF in February and as this is not my first visit this time I would like to experience it from the air.
Could you kindly give me a recommendation whether a helicopter or a seaplane tour is preferable?
I've flown in both and they're very different experiences. Comparing helicopters and airplanes because they both fly doesn't even begin to touch the differences. It depends a lot on what you're looking for. For one thing, helicopters can travel MUCH slower, down to hovering, which planes obviously can't. OTOH, that flexibility comes with a loss of stability as the rotors induce a certain amount of shake. I've seen portable gyroscopic stabilizers, but I don't know if you can rent them and they're pretty expensive to buy. Also, unless you're going on a pre-packaged sightseeing tour, to rent a helicopter will probably run you over $1000/hour.
Small planes such as Cessnas have side windows that open; in slightly larger planes the cockpit windows open so you don't have to shoot through the plastic. A 'high wing' plane (wings over the cockpit) is obviously better - otherwise your only shots are of the wings below you. Depending on turbulence they tend to be more stable for shooting than a helicopter with less shake. You'll be traveling at speed though, so you'll need to use high shutter speeds to compensate.
P.S. I remember one of the Twin Otter pilots I used to fly with told me once that he had a guy up with a Polaroid camera. The guy pulled down the side window to take some pictures, but it seemed as if it wasn't working. What took him a minute to figure out was that 130 knots the film coming out of the front of the camera when he pressed the shutter release was whisked away instantly in the draft. Almost as embarassing as the pilot (not the same one) who leaned his head out the window and lost his headset. Had to pull it back in by the cord. Anyway, I digress...