I live in Boston and wouldn't consider the Nine-Zero to be in a seedy area. It's in the middle of downtown, so you're bound to see homeless people, pan-handlers, etc. as mentioned above. But you will see this in any major city. But it is by no means unsafe -- even walking around at night. I mean c'mon...the Ritz is just a few blocks away.

The Nine-Zero is closer to the Boston Common, many of the historical sights, the Charles River, and high-end shopping areas such as Newbury Street.

The Marriott Long Wharf is closer to the harbor, Faneuil Hall, the aquarium, the North End (Little Italy), and the Seaport district with some fun dining options. You can even take a water taxi over there from the Marriott LW which could be fun for your daughter. Without a doubt it's in a nicer area, but it just depends what you're looking to do on your trip. When I go on a staycation in Boston I choose the Intercontinental which is also over by the harbor. I like to escape to a quieter part of the city when I'm done for the day. You'll get a better Boston feel in this area...if that makes sense.

If I were you, I'd choose the Marriott. It's definitely a more pleasant area and you're only a 10 minute walk from the Nine Zero and downtown anyways.