Even though it's very touristy, we really enjoyed the Alkmaar Cheese market and all the ceremony that goes along with it. I'd vote for the second tour, especially with children.

I think I'd agree with that. Edam isn't terribly interesting (particularly for kids though it's a pretty enough place), and the main cheese store there touristy and overpriced; it might be nice to skip it entirely, but it's on both of your possible tours. It would be better paired with the real cheese market at Alkmaar.

If you want to buy some cheese, though, you may find that buying cheese is a better deal at Schipol in the small supermarket there, where they sell the same cheese about 15% cheaper than in Edam. That's what I found when I was there in March.

I visited the windmills at Kinderdijk, which I thoroughly enjoyed, but I haven't been to Zaanse Schans or Schermerhorn, so I can't speak to the windmills there.

I'm not familiar with Schermerhorn, but have been to Zaanse Schans. Zaanse Schans has an entrance fee for the museum area and I assume that is what is being offered on your tour. They have craft demos (cheese,wooden shoes), etc.
http://www.zaanseschans.nl/

Schermerhorn has some pumping windmills, one of which is open as a museum. No where near as touristy as Zaanse Schans.

Kinderdijk offers more interesting windmills, which are UNESCO listed.

However of the two tours you are deciding between I would go with the Alkmaar one. As Doug say if you want cheese by it either at the airport (where presumably it is suitable for import into the US, or at a supermarket. Same cheese, just a lot cheaper.

Thanks, Alkmaar it is. I think the kids will enjoy the ceremony of the cheese being brought to market.