The options seem pretty limited there -- the cities where the hijacked aircraft departed from, maybe, or the places where they crashed. But isn't it the role of the judge, not some Washington bureaucrat, to consider changes of venue? And the jury would still have to come from wherever the prosecution alleges the crime occurred:
In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law ... US Constitution, Amendment VI
The US District Court for the Southern District of New York may not be the only reasonable place to try the case, but it seems like the most reasonable place to try the case. It's where the most damage was done and where the largest number of victims died.
The usual suspects are still quacking for "trial by military tribunal," of course. Their case is weak. Military tribunals are a wartime instrument. The US declared war on Japan the day after the Pearl Harbor attack. It's now been more than eight years since 9/11 with no such declaration.