When it comes to "an existing building, park, or other piece of infrastructure in the Boston area that they believe makes a positive and integral contribution to the built or urban environment," the Rose Fitzgerald Kennedy Greenway is a contender on all fronts. It not only continues to evolve year-after-year with its expanding calendar of events and maturing tree canopy, but also succeeds at reconnecting the whole of Greater Boston with its Waterfront.
I'd like to nominate the Emerald Necklace as well... I think it's critical to highlight the significance of our parks as positive and integral contributors to our build or urban environment, and the Emerald Necklace is noteworthy among major cities for the precedents it set, the non-vehicular transportation connectivity it promotes, its public health benefits, the cultural richness it lends (arboretums, memorials, museums, etc.), and the communal gathering it facilitates.
I also echo others' nominations of the Isabella Stewart Gardner Museum and the Northeastern University Interdisciplinary Science and Engineering Complex.