Thanks everyone. We ended up going out of Plymouth, so as not to deal with traffic in Boston, and saw a lot!
If anyone else is reading this because you are also thinking of going, here are my thoughts now that I've been:
1) The web site was very big on jackets/layers. - Maybe it was just hot yesterday, but we never took ours out of the bag. We were glad we listened about bringing sunscreen, though.
2) Food was not unreasonable, but you were allowed to bring your own, which we didn't realize.
3) The boat ride out TO the whale area can seem long for kids. If you're not feeling creative, it's a good idea to bring something for them to do while waiting.
4) Bottom vs. top level of boat - more shade on the bottom, but harder to hear announcements over the speaker do to engine noise. Side views are fine from either level. The bottom of our particular boat did have an especially good, though small, viewing area right in front, where you could see to either side. (I noticed this is where the 2nd and 3rd timers with the really big camera lenses went.)
5) If you are going out of Plymouth, there is a very reasonable 10-hour parking lot behind the restaurants/shops near the wharf. (The on-street meters are only 4 hours.) You pay ahead at a machine, and display the slip in your window.