We chartered a private sailboat which held just the six of us and two crew through Morningstar Charters. They took us sailing to St John where we then anchored to swim on secluded Honeymoon Beach and snorkel (they provided the equipment and brief instruction). They grilled us a delicious chicken lunch and then sailed back to St Thomas. They even arranged the taxi to/from the port to their boat on the other side of the island. Had a fabulous time and it was wonderful to have the flexibility, especially with the little ones in tow. (my youngest napped down below on the way to St John). The crew was very knowledgeable and fun. I would definitely recommend an excursion with them.
Again we booked a private tour, here with Carlos Medina of Charlie's Custom Tours (Charlie is the name of his plush van which seats up to 8) which we found on trip advisor. Carlos was AMAZING and jammed so much into our 7 hours with him. We were able to see SO much more than if we had booked a cruiseline excursion, and again he was so flexible with our needs/wants and our little ones. He was a wealth of knowledge of all things about San Juan, Puerto Rico and had boundless enthusiasm so entertained all of us throughout the day. He used every second wisely and was always aware of the time (especially important for cruise passengers) and we were completely amazed at how much we were able to see: went on a mini-hike in the El Yunque rainforest, through a small village and cave along the coast, and a tour of the Castillo de San Cristobal fort in Old San Juan. He even snapped tons of great pictures and emailed them to us right away so we were able to have group/family pictures wherever we went. We had a spectacular day because of Carlos and I can't recommend him strongly enough!
It was a little chilly and overcast so we weren't able to enjoy the beach to its fullest, but it looked gorgeous. I ran a 5K on the island in the morning which was not publicized until the night before when the schedule for the next day is left in your state room. It was low-key and fun but I was disappointed to have to pay for a race shirt afterwards (my choice because I like to get the race teeshirt from different races I've done, but they are usually free).
We rented bikes and had a really nice ride around, except for my 5 year old who opted to go to the kids' club on the island. The bike path is paved and flat so very family friendly. We booked the bike rental ahead of time which I found to be unnecessary- there are plenty of bikes, so if I was doing it again I would not prebook/prepay for bike rentals. And on the Disney cruise website when booking the "bike rental excursion" it said that kids had to be able to ride a bike, but when we were there they had both baby seats for the back of bikes and bikes with training wheels available.