As long as the 9/11 terror suspects are tried in an American court, it doesn't really matter what specific court they are tried in. Nationally, their crimes affected our nation and were against our nation, so they should be tried in our country. Fundamentally, their crimes significantly affected the state of New York so it would be justified that they be tried in the state of New York.
We need to try terror suspects in civilian courts because we can never know for sure without evidence being presented in such a fashion that only a civilian court can allow for if these people are really terrorist or not. To rob people of this guarentee is to allow for a situation where anyone can be labelled a terror suspect and be robbed of this cherished right.