My favorites are:
St. John's - The Eco Hike excursion, or just a beach day at Trunk or Cinnamon Bay (Cinnamon is usually less crowded).
St. Thomas - Mangrove Kayak trip, or Sapphire beach. It's also kind of a fun island to do an island tour. You can book the excursion, or just make a deal with a cab driver on the dock. If you do the tour, make sure to stop at Mountain Top for the over-priced banana daiquiri (Mountain Top is the alleged home of the banana daiquiri).
Hope this helps.