I have been to St Thomas and St Johns a couple of times. There are 2 ferries that run back and forth between the islands. The 1 downtown takes longer than the one up on the north side. Not a big deal unless you get sea sick, the water can get choppy. What we liked to do is spend the days at St Johns and the Nights at St Thomas. Over at St Johns you will find the most beautiful beaches in the Carribean. There is a place to rent 4WD Jeeps to cruise around the island in. You must try that! The island is magnificent! Some of the beaches there have public restrooms and showers. At the end of the day you can have a cocktail and watch the sunset while you are waiting for the ferry back to St Thomas. There isn't alot of night life on St Johns. At night St Thomas rocks! Plenty of nice restaurants to eat at and some great local bars. They are all close together and within walking distance of each other. Make sure you go to the 4 Seasons for a drink. Great view.
Most of the open air spots are cigar friendly and they have a couple of decent B&M's on the island.
You will have a great vacation! If you want any more info, shoot me a note and I will be happy to help.