I've been to both Trunk Bay and Cinnamon Bay...each are equally good but Cinnamon isn't as crowded. If you want good snorkeling and the same great water, I'd suggest Cinnamon.
St John is worth the transports, just to see the beauty of the island. If you have a couple hours to take the island tour....it's fantastic! Tours are sold right off the ferry dock in St. John as well as on St. Thomas.