Are you flying back the same day? Pick the Financial District bus stop (you do know these are bus connectors from the train stops across the bay right?) which is in front of the Hyatt Regency. Then you need to take the BART train from the subway station right in front of the hotel to SFO.
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It is very hard to give good advice based on these 1-sentence question.
If the OP is taking a train from the Sacramento direction, for example, I would advise getting off at Richmond Amtrak Station and transfer to BART, and will not pick anything "San Francisco" in the name on the Amtrak ticket.
So to the OP: would you give an overall picture? Where are you staring from, using Amtrak, that you want to reach SFO airport?
Good point... more info on where they are starting would be helpful.
What train are you taking?
If California Zephyr then it will be punctual as the starting point is Emeryville.
its the best station to check any luggage that you might want - although there are storage racks on the first level of the car to put your luggage. Its where its most accessible.
If you are traveling on the Coast Starlight do check when the train arrives at the station. Its more comfortable waiting at Emeryville station. There is also a good food court area walking distance from Emeryville.
The Public Market
I would not use the Richmond Station if you are going for a longer Amtrak trip. Locals do use it when they are going for train travel for the day such as to Sacramento. If you are just doing that, it works ok as there are frequent trains to Sacramento. (i.e. Capitol Corridor)
For longer distance travel go to Emeryville. There are as said places in San Francisco to catch the Amtrak bus to the station.
If you want more information on Amtrak, your Amtrak experts such as shallow-shoals is on the trip advisor Trains forum. Shallow_shoals is a very good source of information and is the resident expert for Amtrak.
mini: The OP is going to SFO airport from somewhere using Amtrak. It is the opposite direction of you were thinking. They are not starting their travel from SFO. They are flying home from SFO it seems. That's why we asked for a bigger picture of their plan.Edited: 20 August 2017, 23:21