Look into Denis Bay - Genti and Reef Bay - Newfound Bay - Ditleff Point Beach -- all are less visited and more secluded than the popular easily accessible, drive to, beaches. I don't think the proximity to any beach would be important if you are only venturing out rarely. Very few people find snorkeling scary and it is quite easy to float and look underwater with a mask and most kayak trips are in calm water.

This is getting silly,

Look, rent a jeep, get a map and explore. That's what STJ is all about.
The perfect beach is the one that you discover on your own.

Otherwise, hit Trunk. It's absolutely perfect for pilgrims. Huge parking lot, life guards, concession stands, bathrooms and ton's of cruise ship cattle.
They even have a snorkle trail that will keep you from getting lost in the water.

Book a half or whole day kayak adventure through Arawak; leave Cruz Bay, paddle north around the west end of St. John, make a stop at a few beautiful beaches to snokel, have a lunch on the beach (full day adventure) and then paddle home to Cruz Bay. Easy, fun, and relaxing.

Okay, June is a slower month anyway so 'crowds' (a relative term on STJ) will not be an issue unless you hit one of the more popular beaches (Trunk, Hawksnest, Cinammon, Maho) while a cruise ship is in STT. If you want to visit any of those beaches just go earlier or later to avoid the 'crowd' and move on to the next beach as the numbers increase. Seriously, you will find a beach where you are alone and when someone else shows up you can always pull up stakes. No worries, just find another secluded beach.

As mentioned Salomon, Gibney & Denis are all secluded and on the North Shore. If you are willing then I also suggest the Lameshur Bays on the South side. Not very traveled during June but excellent getaways with beach and snorkel. Reef is empty but does not offer sandy entrance to the water. Genti is sandy but you need to take the Reef Bay hike to reach it. Haulover Bay on the far east end is also a secluded beach but requires 1/2 mile or so walk from the car.

If you do not already have one I really suggest the book 'STJ Off the Beaten Track', easily worth its weight in gold and available from this forums shop.

The first year we ever went to STJ we purchased a copy of "off the beaten track", it was and still is our bible to STJ. We use it so much we had to purchase a new one last year as the original was so beaten up! I HIGHLY recommend getting a copy of this book and using it for your exploration of the island. It is so well written and literally gives you step by step directions to get to certain beaches right down to "look for the ______" and take a left! An amazing book for first time travelers and the seasoned traveler.

You'll find Kayaking on the Cruz side of the island heading toward East End. You can rent equipment there and the water's calm in Cruz bay. It's a great way to spens a day/

If you're new to snorkeling and kayaking, I suggest you check http://www.viecotours.com. They offer a kayak snorkeling trip from Caneel. I've been on several of their trips on STT, and all their guides have always been excellent and very knowledgeable about the area.

Rent a kayak at Cinnamon Bay and head to Whistleing Cay for snorkeling and exploring. We did that in 07 and plan on doing it again. You will most likely be the only people on the island. it was great snorkeling and a cool way to spend the day.

Thanks so much for your helpful responses!