Jennifer, thank you so much for posting (and explaining) this. I have wanted to go to Burlington for ages, but it seems so difficult to get to. It's not clear, though, on the Blue Line schedule, which stop is downtown Burlington. I would also be concerned because the Vermonter gets to Essex Junction so late--and I would be afraid of trying to find a bus that late somewhere I had never been. Did you do it when you were out here in the east?
The ferry looks like the best bet, but of course it's only summer, and unless I'm reading it wrong, it looks like the train gets to where the ferry is about two hours earlier than the ferry leaves, so you're sitting around in the summer sun (even up there it would be hot) out in the middle of a field or something with nowhere to go in and get out of the heat.