Introduction to whale watching: Another highlight of the New England Aquarium is to go out to sea to watch whales. The best place to watch whales is Stellwagen, an undersea plateau formed during the Ice Age in the Boston National Marine Sanctuary. It takes about 1.5 hours to sail from the pier to this best whale watching spot. After deducting the round trip, the actual face-to-face time with the whales is about 1 hour.