I parked in an ACE parking lot next to the Midway for $10 (prices as of June, 2013). It was worth it to me. It is located at 910 N. Harbor Drive (Phone (619) 233-6624).
The ferry is $8.00 and bikes (and trikes) are free. You can check their schedule online.
Here I am at the San Diego Harbor, Broadway Pier first in line to board the ferry with my Gekko FX trike and hoping that she will fit through the gate, down the ramp and on to the ferry.