If the prices are higher when you click on the link, try changing the dates. However, it is also very likely the prices have gone up. You don't need to book directly from the airline. Your favourite travel site/agent is fine. Keep in mind, you probably need a place to stay: hotels can look very expensive when your flight is cheap. For future postings, click on the "travel" label at the bottom of this post.
These prices are very cheap and will not last long (especially from Moncton). Take some time and shop hotels, however, as they can get pricey. Lonely Planet list some guest houses for the financially challenged.
-Burlington, Vermont, to San Juan, Puerto Rico, in the Fall: $308
-From New York in the Fall: $214. in the Winter: $224