http://www.cruisecritic.com/ports/area.cfm?area=13
I think a cruise of Mexican Riviera round trip LA or San Diego is a wonderful idea. We did it in Dec 2004. You can also round trip SF but it would be 10 or 11 days. Come 2008 there would be no more ship from SF because the lines lose money on the SF roundtrip route.
Cabo San Lucas / Los Cabos is TERRIFIC. Cabo San Lucas is the newer sister of the twin towns which are 15 or 20 miles apart and linked by a highway served by local buses. Along the highway there are many expensive resorts, esp the older ones but more elegant ones.
Cabo San Lucas itself also has developed a more concentrated resort area, but the sea is very rough (facing Pacific), therefore the beach is NOT swimmable at Cabo. The swimmable beaches are more towards the town of Los Cabos.
There is a very modern Marina at Cabo and you would see Mega Yachts docked there in winter time, all carry US plates. Deep sea fishing is BIG in the area.
If you go between Jan and Mar, you can see a lot of Grey Whales and some Humpbacks just outside the harbor of Cabo San Lucas - much cheaper to do whale watching there than in Maui!
The town Los Cabos is one of your typicle Mexican town, and there is a small town full of artists nearby.
Like most towns in Mexico, Matzalan has an old town and a new town. The old town has some very interesting archetectures and streets, as well as a big church plus the square. The new town is several miles away called Golden Zone, where all the hotels and time-sharings are. We did not visit new town. We like the old town a lot. Matzalan also is a big port - we have never seen these small size Japanese cars parked at the Cargo Pier. It is quite a scene. I believe because Matzalan has more than just tourism, it is wealthier, and newer, also cleaner, than Puerto Vallarta.
Puerto Vallarta also has an old town and new town - and they go opposite direction. There is a big old WalMart just accross street from the cruiseship pier and we use it as our "marker" when we take bus back from the old town. :) The old town of Puerto Vallarta is very charming - it has a seaside boulevard full of very beautiful sculptures - we were very impressed by the quality of the art pieces. One needs to take the bus to the old town and then one can walk all the way to the old old town which is at the edge (sorry, forgot it is East or West) of the town where one can see lots and lots of very interesting stalls selling all sorts of beautiful crafts. The silver crafts in Puerto Vallarta are of very very high quality - very delicate and very artsy - far better than those one would find in Cozumel, for example.
If you want my 2 cents - they are all well worth a visit and a cruise would visit them all on one sailing. After that you can decide which town you would want to go back.