It looks like New York City is out (as it should be), so leaves really only leaves Virginia. There are two federal courthouses in the area. One of these courthouses was used to try Zacarias Moussaoui. This particular courthouse is in Alexandria, Virginia. So let's take a look at this courthouse.
Here are pictures of what is around this courthouse:
This a condo building. I am not sure exactly how many units are this building, but I would say 200 to 300 judging by the size of it. I have a friend who lives in this building. Another person who lives here (or least used to), is the former captain of the USS Cole. I think that he won't be too happy to have al Qaeda this close to his home.
Less than one mile (6/10 to be exact) is King Street metro station. This station also has Amtrak trains as well. Now, if you look at the attached map to this station you will see that it is two short stops to Ronald Reagan Airport and five or six stops to the scene of the crime, The Pentagon.
These are office buildings and a hotel. There is also the US Patent & Trade Building within blocks of this courthouse. During the day, this is an extremely busy area. People going about their lives. Is this really better than blocks away from ground zero? Now, maybe I am baised as I live less than 20 miles from here, but I didn't like it when it was in lower Manahatten either.