Ken your ports of call are very doable on your own. Bermuda - get an all day bus/ferry pass, inexpensive then head to Horseshoe Beach,-beautiful beach with good snorkeling the underground caves(so neat), the botantical gardens, or just stroll around Hamilton. If you are into history head up to St. George. In San Juan you can just grab a cab to a beach, or stroll around Old San Juan and Fort El Morro, El Yungee Rainforest is breathtaking, i would do a ships excursion for this. In St. Thomas- beautiful beaches to choose from, if you want to do some snorkeling then i would suggest you take the ferry over to St. John Island for the day. If you want to stay on St. Thomas proper and hit the beaches so many to choose from - go to Virgin Islands Travel Information
for beach & ferry info - my personal choice for a beach on St. Thomas would be Sapphire, if you want to do some shopping, St. Thomas is the place to do that, another cool thing to do in St. Thomas if you have a couple of hours to kill is to take the Paradise Point Tramway, short walk from Havensight Pier ( if you dock there), the view from up top of the harbor is spectacular, there is a botanical garden, bird sanctuary and some cute shops up there.
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