Where is Honnouji?

//For clarification, I mean Honnouji Academy as seen in KLK, not the actual shrine outside of Kyoto. 
I used to think it was in the bay by Nagoya, Japan, but I slowed down and carefully looked through a little clip from the second opening and found it’s actually in Tokyo bay.

//By the way, it’s freaking huge. Look at that! It’s a huge part of the bay.

//That tiny dot in the middle is Ryuko standing in the middle of the courtyard.