If you really want to see St. John, don't hesitate for a second to go out with Island Roots. Captain Ivan took our group into consideration (grandparents and kids aboard) when he picked our stops for the day. He was so patient and kind with the kids, and very professional. He also gave us a lot of interesting history on the island while we cruised. The boat itself is pristine, well appointed, and very comfortable.
We circumnavigated the entire island on a picture perfect day. We saw everything and snorkeled a lot; Caneel Bay, Trunk Bay, Cinnamon Bay, swam with the sea turtles at Maho Bay, had lunch at Lime Out (don't miss this, especially with kids- the unique floating lunch spot has awesome food and drinks, and Frederica the mutton snapper who thinks she's a dog, was a highlight for all!), and capped it off with some swimming/snorkeling at Salt Pond Bay.