Morro Bay is a crappy place to keep your boat because there are no real destinations there other than San Simeon or Port San Luis. Anything else is 100 miles either uphill to Monterey or around Point Conception to Santa Barbara and beyond. I't also chilly out on the water about 364 days a year. It's relatively cheap (about $8.00 a foot or $250.00 for a mooring) IF you can find a berth. Morro Bay is beautiful.
Ventura has tons of destinations, warmer water, a reasonable amount of wind and swell, but it's more expensive to keep your boat there, IIRC $12.00-$20.00 a foot depending on the marina and there are no moorings and no anchorage. Ventura/Oxnard aren't beautiful.
I would chose Ventura if I had to make that choice. I lived in and around Morro Bay for 25 years.
+1 everything said above.
Morro Bay is the destination, Ventura is where you park your boat between destinations.
Here are the costs you can expect to pay to keep a boat in the water in Ventura:
Slip fees - $12 to $13/ft and an additional $190 -$250mo if you plan to live aboard. BTW, living aboard is the best value as the boat expenses become your home expenses.
Bottom cleaning - $1.50/ft per month
Insurance (prudent anyway but required by marina) $500 to $$$$$ per year depending on coverage, boat value, cruising area, credit rating etc. etc.
Property tax - 1% of value of boat per year
Bottom paint every 3-4 years - ~$50/ft if the yard does the work, $15 to $18/ft DIY assuming about a 3day turn around(welcome to SoCal)
The above does not take into account the general costs of upkeep such as varnish (refresher coat every 6mo to a yr), polish and wax, rigging, engine etc etc.
For all that you get a potential 365 day sailing season, the best cruising grounds in California with the Channel Islands just 20 miles off-shore, Santa Barbara 25 miles North. LA, Newport, San Diego and Mexico to the South (downhill there, beat back).
Personally, I think it's worth every penny.