Hi, mollyllt,
Outside of the major metropolitan areas in the Highlands, there is not a whole lot for children. Especially your four year old. In addition to a "Nessie" cruise, you may want to try a dolphin tour in the Moray Firth, or just watch for them below the Kessock Bridge.
You also may want to consider staying at or visiting a working farm. My son really enjoyed bottle feeding lambs when he was eight years old. The Isle of Rum, accessible by boat from Mallaig or Arisaig, would be a good place for an overnight. The Rum Bunkhouse has three four person rooms, with bunks. There are red stags wandering about everywhere, as well as wild ponies and goats. There are a couple of easy hikes, and a great community center with meals and games. Also, Kinloch Castle would be fascinating for the kids. (And you and your husband as well) Rum can also be done as a day trip out of Mallaig, with enough time to visit the castle.
The city of Inverness should have a few things to keep the interest of the kids. There's a branch of the Scottish restaurant (McDonald's) in the center of town, plus the Eastgate Center mall, if they're missing that aspect of American life. There are some walks in town that may be of interest, especially the Ness Islands. The tourist information office (TI) should have some brochures on children friendly activities in the Inverness area, or should at the very least be able to make some recommendations.
The Fairy Glen and Fairy Pools on Skye should be of some interest to the children, as well as the colorful harbour at Portree. There are eagle watching boat cruises from the harbour, although you're not guaranteed to see anything. AquaXplore, out of Elgol, offers cruises of up to four hours in search of seals (guaranteed), dolphins (not guaranteed), whales (ditto), and sea eagles (ditto).
There is a small animal sanctuary near Plockton, which you may want to visit on your way to or from Skye. It's the Craig Highland Farm, and has all sorts of domestic and farm animals, including raccoons (!), llamas, goats, ponies, cows, and all sorts of birds. It's a bit run down, but the youngsters would love it.
I'd say that your best "home bases" would be Inverness and Portree/Broadford for the greater opportunity for things to do there, and on day trips. There is a really good (and free) museum in Elgin, and also the possibility of more dolphin sightings from Spey Bay. There's a grand beach at Lossiemouth, but you'd need to bring along buckets and spades for maximum kid fun. There are also several ice cream vendors along the beach front, and another of those Scottish restaurants in Elgin, which you'd encounter on the way back from Lossie.
You may want to consider picking up some board games which are specific to Scotland, so that the kids have something to do in the car or in the evenings. If they have any hand held electronic games, it may not be a bad idea to bring them along for the car rides. Kids usually aren't as interested in spectacular scenery as we are!
You may wish to be careful about what you watch on television in the evenings. British television is much more lax on profanity and nudity than here in the U.S. The Saturday national newspapers have television listings for the following week. You can always watch BBC ALBA, which broadcasts mostly in Gaelic, even their children's programming.
Finally, you'll be there at the start of midge season in the Highlands. If the weather has been particularly damp prior to your arrival, you may want to invest in midge hats, which are available at most outdoor shops, like Graham Tiso, Black's, and Nevisport. They pack in to a small pouch, and are easy to carry. You also may want to invest in some insect repellent, like Avon's Skin So Soft, or Repel, for the exposed areas.
Best of luck in your travels, and have a wonderful time on your holiday!
Mike (Auchterless)
