My experience with whale watching out of Boston is that we went straight out for 2 hours (I thought we were going to end up in Europe, lol). It was very choppy and many, many people spent the entire trip lying on benches. We saw a couple of tails, but that's about it.
Whereas in Juneau (I highly recommend Harv & Marv) you can see land the entire time, it's very calm and whales galore -- we even saw a pod bubble-net feeding, which was amazing.