we've been to St. Thomas 3 times, and been to St. Maarten 3 times by ship (with another weeklong stay on St. Maarten). Agree that Trunk Bay is really a schlep, but we did it once, but it ends up being a total of 4 hours of round-trip transit--or at least when the Magic docked over at the new dock instead of havensight in April 2005 it took that long. Did it ourselves, as we did for magen's bay and as we have done for orient beach (the 9 & 11 yr olds, if mature, will be fine, DS was 9...I told him about it ahead of time, he knew in advance that girls dont have what boys have, and the rules were no giggling and for goodness sake no pointing--and if he saw anything that he was curious about he should just quietly ask me. there was one "hey dad, look..." moment, but as I replied, "I'm way ahead of you, yeah, incoming at three o'clock").
island tour--you mean something educational or cultural instead of a beach? semi-kidding. semi. that's got to be your call. but indeed, if you want to snorkle, magen's bay will not be ideal, and trunk is a schlep. I've also read many endorsements to go on your own to cinnamon (sp?) bay for snorkling, but again, that's over to st. thomas. we enjoyed getting the view of the island on st. thomas when we rode in the open air cab to magen's bay--you go to and through charlotte amalie, then up and over the mountain in the center of the island--awesome views and photo-ops -- on the way. both of these islands are ideal for going on your own as they have a decent amount of infrastructure, so getting a cab back is no problem--though traffic on st. maarten scares me from going over to the french side capital, marigot, into the afternoon--my fears after staying on the island for a week and sitting in some serious backed up traffic around 4 in the afternoon. but orient bay, though on the french side, is near enough to the port that it was not a worry to me at all.
my plans for my next eastern--on
RCCL next spring--beaches both days, though I also want to see a thing or two in charlotte amalie so I will make it early to the beach and then back into downtown--got to be up early for immigration anyway, and compared to my usual weekday, when I'm up at 5:15, getting up at 6:15 or something like that for customs is still "sleeping in".
good luck and enjoy--disney magic on the eastern is my all time favorite combo of itinerary and ship of all of my cruises to date.