If the price for your flight is a lot less expensive flying into Oakland, go ahead and book it. It will cost you about $10 - $20 more for your taxi ride (depending on traffic) to the San Francisco Pier. Coming from Oakland you will also have to pay the $5 Bay Bridge Toll that you don't have to pay if you fly into San Francisco.
Two other options: Both SFO and Oakland have BART access into the city. Both airports also have Super Shuttle. They charge a flat per person rate with 3 or 4 stops.
What hotel did you get on the Embarcadero? That's a great location and close to your ship. The price you quoted is really good.