It is indeed shot on location at the Pearl Harbor visitor center. And you do in fact see both Ford Island and the port apparatus!
I've been there twice and the area has changed GREATLY since this was filmed. Here are some comparison shots. Sorry these are a little large...
First, here is a shot of Rick and his limo in the parking lot. Behind Rick you can see some bushes that are at the end of a hill leading off to camera left.
Below is the modern Google street view from the parking lot. I can't get the camera to be in the same exact spot but this is close. The same hill is still there, but the bushes have been removed. That white building in the center of the photo and its small parking area are new.
Rick talking to the other limo driver. Behind the limo driver's back is the entrance to the parking area.
Same parking area entrance, between the white van and the red and white striped pole.
The two shots below are also real. That is the dock the tour boats leave from to visit the Arizona Memorial, visible in the distance to the left of the tour boat, and the land on the other side of it is Ford Island. The Navy ships are out of camera view to the left, so you don't see those. The concrete structure Magnum is running into in the second photo is the theater and museum.
Google view of the dock.
This area is NOT, however, visible from the parking area where Rick is! Magnum shouts to Rick, "Stop him!" and Rick is apparently able to see Magnum jumping off the tour boat, but this is impossible! Below, the red X in the parking lot is Rick. The green X at lower left is Magnum! But he's acting like Rick is right on the other side of the building!
Here the limo driver is about to get into his car. In upper right you can see two buildings. These buildings are still there.
The camera lens used in the show made the shot look very compressed, making the buildings look much closer than they are in real life. This Google street view is taken from across the highway in another parking area, not the one in the show. The two buildings can be seen in the center.
Cropped image of the two buildings as they look in the show:
Now here is where they might have gone off site. I cannot find that building nor remember seeing it there. Perhaps the whole thing was torn down and renovated some time after 1980? It seems weird that they would go off site for just this one brief shot.
EDITED TO ADD: I just saw your other post in the Rubber Chicken thread. That is definitely the same design as the Tree of Life sculpture, but that is a freestanding slab, not part of an elongated thing like we see in the show. It's standing by itself inside the complex, not next to a parking lot. And it's white, not beige. Could the modern Tree of Life be trimmed down (so to speak) from the original one that was by the parking lot? And this still doesn't explain the building in the show to the right of the old Tree of Life. Below is a photo of the TOL as it now stands. The theater is on the right, on the far side of those benches.
Here is a map showing the modern day Tree of Life location. Nowhere near a parking area. It's circled in green, not exactly where the red pointer is.
OK, back to the parking lot! Here the limo guy drives away...
...and here Rick is chasing after him. The parking lot has changed so greatly since then that at first I thought the actual car chase WAS filmed off site -- but it wasn't.
Magnum and Rick are about to get into their car. The car has not been moved, it shows the same background as before when it was verified as in the Pearl Harbor visitor center parking lot.
There is a fast cut to a closeup of the guys getting in the car. I thought this was the part where they switched to the "other" parking lot, but it isn't -- all elements/details of the ground are the same. Same manhole cover by the left front tire, same bits of trash/etc on the ground.
Magnum gives chase through the same parking lot as the limo guy.
Looking in the same direction Magnum went, this is the view today.
Thus, you might know that Magnum PI had a dazzling success in my country... back to the 80's !
Thanks for having dissipated this 'shadow zone' once for all 
) there, it was really difficult to figure out if the sequence was filmed at the genuine place or not. 
