bdokeefe - Great advice.

Thanks again guys for your advice! Given the singularity of our trip to Half Moon Bay I decided to have us skip the 1 night stay there, and just have us stay an extra night in SF. Then we will hit up HMB on our way down the coast on Saturday morning. Since a number of you mentioned HMB lacking in tourist appeal, I didn't think uprooting ourselves with luggage, etc. for the 1 night hotel stay made sense anymore. Gotta stay flexible!

Point Lobos is a must as others have sai!

I just want to add that for a safe beach to play on for your kids, I prefer the beach at Lover's Point in Pacific Grove. It's a sandy cove that is very protected... a few rocks to walk on with small tide pools that entertained me when I was small and also entertained my boys at that age. It's scenic, usually with sail boats in the bay and should make for a pleasant few hours. As a bonus, there is an ice cream stand!

I spent last Sat at Half Moon Bay- first time there. It was a beautiful sunny afternoon. Did some shopping in the downtown area, which had several nice shops and restaurants- I didn't see anything that would be very interesting to kids.

After a bit of shopping, we drove to the Harbor area and had lunch at the Half Moon Bay Brewery. They have a nice outdoor dining area, views of the ocean. There is a fire pit for those chilly days or evenings.
We had some great salmon fish and chips.

If you walk down to the harbor, you can buy fresh crab off the boats and you can have them cleaned and steamed right there. Might be a fun picnic lunch with kids

Found a nice beach to walk on a little south of town- but there were big globs of jelly fish on the beach in a few areas.
I really enjoyed seeing the area- will be back.

Another way to do it would be to take the Amtrak bus 6011 back to Oakland Jack London at 7:45AM from Ferry Building. Take the Coast Starlight south to Salinas and the 3611 bus to the Aquarium. The bus arrives in front of the aquarium (MYA) about 12:45PM. You might even want to board the northbound CS in Salinas instead of at Oakland or Emeryville in the late evening.

If you go with the rental car down Rt. 1, you could stay south of HMB at the Pigeon Point Lighthouse. http://www.norcalhostels.org/pigeon
It is not fancy but it has a kitchen so you can cook an evening meal. DW and I have stayed there twice.
With the Amtrak option the bus leaves the aquarium at 4:45PM with a guaranteed connection to the northbound CS (14) at 6:28PM in Salinas.

Our rental car for the 4 full days with taxes only amounted to be $109 I think. So, for the convenience of stopping here and there and everywhere in between SF, north of SF, and Monterey, it was a screaming deal. Although free, (my husband works for Amtrak) the freedom and convenience definitely win out here. It was hard enough to get him on the train to begin with! :)

Lynni, thanks for the beach recommendation, I have written it down and hope we get to make it. Sunbum, thanks for the dining recommends. We will most likely take in lunch during our visit in HMB.

Since your husband is a surfer, a stop in Santa Cruz might be in order as well as a visit to Carmel's city beach--lots of surfers in both locations. Santa Cruz is unofficially Surf City (some town down south grab the name for itself officially I believe.) Carmel Beach is huge and kids seem to enjoy it as well as lots of dogs.