Lots of marinas.  They are all technically full, but if you call at the end of a month and are ready to go you might find they don't pull out their waiting list.  Coral Marina in Ensenada, sixty miles south, is a great marina with lots of slips.  Cruiseport, same location, isn't as fancy but in down town.

I forgot one that generally has availability.  It is the Chula Vista Marina.  A nice marina but very far south in the bay.

Also Pier 32 in National City, also in the southbay, but not as far south as Chula Vista. ​https://www.pier32marina.com/