I suppose the Blue line might be a better idea, as it brings you right to Faniuel Hall. I was just thinking the complications of figuring out which bus to take to the blue line station. How I wish they would find a way to move that closer.
I am assuming that this is still going to be fairly cool out, and in the evening. So I am not going to recommend the boat. That takes a lot of waiting, too, although that could be part of the fun if you are doing it in the summer. Quincy Market/Fanieul Hall would be great for a 9 year old - it's a big food court and shops that are not all chains. The Aquarium is across the street, and a 9 year old would love to look at all the boats parked there (I know I still do!). If you have a little more time you can do the IMax theater there, go to the North End and get a cannolli at one of the pastry shops, or walk over a few streets to Washington Street to absorb the big city environment (it's a very safe area - lots of businesses). Or you can walk over to Rowes Warf, where they often have some interesting sailing ships parked there.
I wouldn't worry about time - two hours is more than enough to get over, grab something to eat, walk around a bit and get back.