So on a whim I spread the search down the line into Tokyo Bay, and BAM, found it.
Wikipedia gave the low-down: The Tower of Wind is a ventilation shaft for the Tokyo Bay Aqualine- the world’s longest undersea tunnel for cars, which cuts under Tokyo Bay from Yokohama to Chiba.
Umi Hotaru means ‘sea firefly’, again a great name for a Miyazaki movie- so named because that’s what it looks like.
Helicopter shot, Sea Firefly sea airport.
FACTFILELocation – Tokyo BayEntry – Not to the Kaze no To, but yes to the Umi Hotaru.