Custom House is great, we did a preview when they were developing the project since both DH and I had offices right next door. For years we would have all sorts of tours parading around our office buildings during the "tourist season". I've always loved living in the middle of all this history. Downtown Boston, espec the area around the Custom House has been a huge construction site for about the past 15 years (have you heard of the "Big Dig") and it's just about getting down to the final stages. Parking in the Custom House area is usually pretty difficult and expensive, except during the day on weekends (since it is near the business district) you may be able grab a parking meter within a block or two.
Just some quick things to keep in mind, if you are trying to visit anytime in the month of May you could have trouble gettting reservations, graduation time at all the schools in Boston pretty much books up most of the major hotels with parents for years in advance! Also, not sure if they have reconfigured but when we previewed the Custom House timeshare they only offered one bedroom units. At the time they told us that they traded as two bedrooms due to the high demand. That said, it's a beautiful location, right by Quincy Market and about a block away from the Marriott Long Wharf and the Aquarium. With young kids you will enjoy the Children's Museum and the Science Museum is within about a mile across the river in Cambridge. If you are looking for history, check out the Freedom Trail, it will probably take you the better part of a day. The Duck Tours "quack, quack" are a must do! A slightly more irreverant view of Boston from both the land and the water. The "T" is pretty easy to get around on but Boston isn't that big a city, if the weather is good and you have a stroller for little ones you can walk pretty much everywhere. As a previous poster had mentioned Harvard and Harvard Square (about 2 + miles) have lots thats interesting but it isn't as tourist friendly as downtown Boston. Most of the "what to see" is a little more hidden and less geared towards young children. Plymouth Rock may be a major let down after an hour and a half ride but Plimoth Plantation (a colonial recreation village) is interesting. To make the ride up to NH and Maine is only about an hour.
As far as restaurants go Durgin Park is interesting, old fashioned comfort food, Legal Seafoods (many all over the city) is great although can be pricey for seafood. Pier 4 runs hot and cold but it is the traditional "special occasion" restaurant on the water (food can be so, so but the view is very nice). For Italian food you are right near the "North End" where there are many amazing places. "Mother Anna's" is really good and easy to walk to but there are many, many, many others. For shopping there are a couple of malls within a mile or two. Cambridgeside Galleria is just across the river (near the Cambridge Marriott) with some good restaurants and also the Prudential Center and Copley Place (in the other direction) have great restaurants (and another Marriott) and shopping. Hope this helps.
