We are a family of 6 plus a one year old and would love a villa or house with 4 bedrooms. Not interested in partying or night life but would love access to coffee shops or restaurants. It would be great to have golf, fitness, private pool, beach. Would love to try whale watching

What is the month of your trip? As far as whale watching opportunities and also the weather.

Forgot to say we are hoping for Dec 24-31 give or take a day or two. Limited availability but we do have some choices. Would love to see whales, and have a house or villa or condo to ourselves. Not sure if we should be in a gated resort (Punta Mita) or not

I've been to Punta de Mita but only on a day trip when I stay in Puerto Vallarta (you'd use that same airport, PVR). Sorry don't know anything about villas or gated community or resorts out that way. I just rent an apartment or condo downtown in PV. In Los Cabos I've only been to Cabo San Lucas, again stayed at a hotel downtown no villa or resort so I'm not much help. Christmas holidays are popular and often prices are about double those couple weeks for lodging. Weather should be fine both places.
buena suerte/good luck!

If you are willing to rent a car and prefer to be away from lots of people, I would go with San Jose del Cabo. Whale watch season starts mid December.

Agree about San Jose del Cabo..for me it is far more compelling than Cabo San Lucas which I did not like all that much..
I'd also take a look at La Paz.

{great to have golf, fitness, private pool, beach}

I would look at both places and see what kind of rentals you can find that offers this. What do you mean by "fitness"? Being near golf might swing the vote.