Since OP mentions Oakland, he's probably on the San Joaquin, which doesn't go to San Jose.

I would say that transferring to the Amtrak bus is the easiest option. The buses are timed to meet the trains, so it should be seamless. I personally would have no problem doing the walk from the station to the hotel at that time of night. It's a busy area. Just be aware that the walk is uphill. If you don't want to walk, flagging down a cab shouldn't be hard.

Another option is to take the cable car, which goes from the Powell Street station, and will basically take you straight to the hotel's doorstep. It's expensive for individual rides ($7) but if you are planning to buy a Muni pass then it is included. I believe the cable car runs until 1 AM but I'm not positive.