you're going to get hit hard with ppl telling you to skip st. thomas and just stay on st. john. fodorites love st. john! it's wonderful but pricey and most seem to stay in a villa. i like st. thomas quite well though. lots of dining options and things to do. there are some very busy areas to be sure.
take a look at www.secretharbourvi.com - condo style, directly on nice beach with good snorkeling, a very good restaurant and small but fun beachbar. sh is on the east end of st. thomas near red hook (under 10 mins). from red hook you can catch a ferry (every 30mins starting a 6am ending at i think 10pm) to st.john. 20 min ferry ride. and Yes you can enjoy all the beaches on both islands. all beaches in the carib are public! (well up to high tide mark)
which ever island you choose you're probably going to need a rental car. some st.t agencies will allow you to ferry your car over to st.j. some will not. once on st.j you would have to have a car/jeep to get to the beaches. or take a taxi to caneel bay resort for the whole day. they have 7 beaches with snorkeling on their property and restaurant open to public.
other beachfront hotels on st.t would be the ritz$$$, bolongo bay (younger crowd, more bar action), wyndham sugar bay which is all-inclusive, or marriot but it's close to charlotte amalie, the main town, & i would only stay in the morning star section of this resort if at all. <they do have the one of my favorite all time restaurants on site though - havana blue.