It depends on your taste. Do you like to snorkel? Do you prefer crowded beaches with lots of vendors or secluded beaches?

Personally with only one day on St. John, I would opt for Trunk and roam around Cruz Bay. Trying to hit too many beaches in one day will be a stretch. On STT, I would go to Coki (go in the morning when less crowded), Magen's (also earlier in the morning to catch the good snorkeling on the far left side) or Sapphire Beach.

2 days on STT would have me going to Magans Bay one day - just relax and let the beach servers take care of you! I agree with Coki on the second day if you enjoy snorkeling.

On STJ, I'd recommend going to Trunk in the morning then move over to Cinnamon in the afternoon. A couple of hours on each beach would be worth the effort of moving. Cinnamon is the largest beach and is really beautiful. Trunk simply can't be missed.

Good Luck! Have Fun!

I also agree with megans. get there early, there will be less people. I like sapphire beach also, the color of the water is amazing. On St. john I like Maho. It's a little further down the road than cinnamon and trunk so usually there's less people there and it's right off the road and very easy to get too.
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The suggestions made by other people are perfectly good suggestions. I guess that my suggestions would be based on where you are staying and whether you have a vehicle. The beaches on St. John that were previously mentioned are all along the north shore, so if you are staying on the north shore or in Cruz Bay there are plenty of taxis that will take you there. If you are staying out in Coral Bay, there are a different set of beaches that I would suggest, and the issue of transportation becomes an issue.
I'm not as familiar with St. Thomas, so I'm sure of the beaches or restaurants, but the beaches mentioned previously are all nice.

If you like to snorkel and want to take it easy, go to Sapphire Beach and then you could hop over to Red Hook for some food, bushwackers, painkillers, whatever. Sapphire is a really nice beach....i personally like it there.

Megans is pretty, but it's not a real snorkeling beach, although somebody has posted that there is snorkeling somewhere there, just can't remember where.

Coki....you'll definetly get a taste of the islands :o) There's really good snorkeling there and there's some places to eat. I'd suggest the Mailman where you can just hang.

It just depends on what you're really looking for.