Tri-City & Olympia is gone and I believe California Northern is back to serving Alstom. There were other customers on Mare Island, but Lennar forced them out because they want the property to be strictly residential/office/retail, with no industry. There has been talk of Alstom leaving as well.
By the way, the track from Flosden, through the big cut, to the east end of the bridge that goes to the island is the last remaining piece of the San Francisco & Napa Valley electric interurban. One of the Navy's GE 80-tonners from Mare Island now belongs to the Napa Valley Wine Train.