We are doing the same itinerary- I haven't done this via cruise before, but I know Tortola/BVI and St Thomas well. We are likely not booking any excursions-- we got married/honeymooned in these islands and want to explore old favorites, show our son where we were married, etc. We will come up with a loose plan but also see what he is enjoying, what the weather is, etc. Because I am comfortable with these islands I feel OK not booking an excursion, and would say anyone would be OK getting a car to their destination there (I wouldn't say that about every island).
Sounds like a busy, exciting trip! So maybe some relaxing beach time would be fun without excursions if you don't see anything you like?
On STT, your boys may enjoy Coral World. It's a relatively small ocean park-- they rehab sea turtles, have some touch tanks, and you can see a lot of sea creatures. Disney has excursions here or you could easily taxi there (buy your tix online first though). They have a restaurant and there is a public beach next door (Coki Point) so you could make the day of this event. They have a neat semi-submarine hour long ride to see creatures beneath the surface. The additional things to pay for at Coral World are not necessary if you wanted to keep it to admission only. If you don't want to beach there are two different experiences to see the islands from the top of St. Thomas-- sky ride and mountain top, which the boys may think is cool. There are many companies for private tours on St Thomas as well, you can make the day your own or see what they are offering for something different. You can also be a day guest at the Marriott, not far from the docks, to enjoy their beach and amenities.
Megans Bay is another lovely beach that is very calm waters with lunch options-- our 5 year old is also working on swimming so I am in the same mindset. If you go there, ask the driver to stop for fresh milkshakes here (you can add alcohol to yours):
https://www.tripadvisor.com/ShowUse...mous_Delite-St_Thomas_U_S_Virgin_Islands.html
On Tortola Disney has excursions for just lunch and beach, or you can taxi to any of the beaches yourself. You can also stay on the ship and enjoy quieter times that day!