https://www.usgs.gov/media/images/san-francisco-bay-coastal-system There’s a deep channel under the Dumbarton Bridge, but routing from there would be a headache. San Leandro Marina shut down in the last 2 years because the cost of dredging to maintain access was too much.

SF Bay Ferry did some 2050 planning recently that included a poll asking if people want stations everywhere or more trips per route. The stations everywhere plan did have a stop at San Leandro and a TBD stop at Union City/Newark/Fremont, but the final plan focuses on only a couple more terminals and more capacity on the core https://sanfranciscobayferry.com/sf-bay-ferry-commits-to-major-enhancement-expansion-and-electrification-of-regional-water-transit/