Magan's Bay was very easy to do, in that you step off the ship, get in a big open taxi that takes you to your destination, and then the reverse. So 1 transportation element involved. Note--I did it from Havensight Dock, DS was 6.
Trunk Bay we did from the new Crown Bay (is that the name of it? the new dock being built on the other side of downtown charlotte amalie). from that dock it was slow to fill a taxi, and a long ride to red hook that we would have missed, so we took a smaller cab after the cabbies fought (really) to downtown, got on the smaller, rougher riding ferry, then a cab to trunk bay. and upon the return, the cab from red hook made a stop first at havensight, where the majority of people were going, then to downtown where the HAL tenders were, and then finally to the
DCL dock location. It just felt like planes, trains and automobiles, and it was a haul, esp. for DS, now 9.
Maybe it would feel easier from Havensight. Bu you can't just add three travel times, there is also transfer times because you dont get out of a cab just as the ferry leaves, and at least I don't like to cut things close, so maybe try to make sure there is a cushion of time. And such concerns go away if doing these treks on the cruise line's excursion.
They're both gorgeous places--I actually got rained on at Trunk Bay but I won't factor that in to any recommendations--I just feel that with about 3 modes of transportation from ship to shore at trunk bay, it is a bit much to do with children (and I admit that is a generalization). But our experience was a time to go ship to beach of probably 1 hour 45 mins. each way, and as I say some portion of that was because we were not at havensight. If St. Thomas was one of those stay in port until 10 at night, then maybe I'd feel differently, and If I was at St. Thomas for a land based vacation I'd be more inclined to make the trip because the "get back to the ship" issue would be removed, and so even w/ children you might build in a distraction of maybe getting them an ice cream in the little town by the dock at st. john--but really, didnt feel like I had time to do that while making the trip on our own.
I'm going back 3/07 on the Magic, and I plan to do one of the other gorgeous St. Thomas beaches that I have not experienced, and hopefully we will be at havensight where the cabs fill faster from more ships, compared to just the Magic and the later arriving HAL ship (was either the Zuiderdam or the Westerdam, forget which one).