E94 is usually parked behind Building 210, the NPS administration building, but sometimes is out in the Visitor Center lot. The park is in the process of upgrading the facility at the Great Kills Park Ranger Station to store it there, but that won't be completed for another few years.
I think I know which building you're talking about on McLean Avenue and Lily Pond Road - the one right on the corner. The NPS was hoping to utilize that building, but no luck.