Bobby - a lot depends upon what you are interested in and what your comfort level for going off on your own is.
San Juan - i would suggest doing a ships tour if you want to visit the rainforest, just for time constraints. You can wander around Old San Juan - just grab a cab, Old San Juan is beautiful and very interesting, or you could grab a cab out to Fort El Morro - its the big fortress on the hill that you will see when you enter the port, again very interesting, you get a great vantage point of the harbor to watch all the comings and goings, also this is a great kite flying destination as it is usually very windy up there. There are plenty of beaches to explore, ask your cab driver to take you there, just negotiate a pick-up time and round-trip fare.
St. Maarten - one of my favorite islands - so pretty. Lots to do here. Beach & Shopping!!!!
if you just want to hit the beach then you can grab a cab to Orient Beach - the most popular beach - lots of goings on here, one section is clothing optional (clearly marked) If you want something a bit more relaxed then you could try Dawn Beach or if you want to see airplanes literally flying over your head you could go to Mayho(sp?) Beach. Last time we were here we decided to take a ships tour on the Golden Eagle Catamaran - we had a blast! you sail up the coast - its beautiful, over to a small island preserve(Tintamar) where you can swim, relax on the beach, go snorkeling, go for a walk, have a mud bath(the beach sand is volcanic and very theraputic) The boat supplies drinks and lunch. Another hugely popular tour is the America's Cup Regatta - you sail on a racing yacht in an actual race, you crew the boat. St. Maarten has great shopping on either side of the island, on the Dutch side, grab the water taxi - really cheap for an all day fare and then just wander around the shops. You need to take a land taxi to get to the French side.