I have a 1990 Jeep with EFI and experienced the exact same issue on my 4.2L in-line 6. In my case, the whistle began during colder ambient temperatures but grew worse over time (months). Also, it only occurred at or near idle when the intake manifold pressue is at its lowest (greatest vacuum). I won't trouble you with all the troubleshooting I did, but will go to the root cause and fix. The exhaust and intake manifolds are VERY close together, even sharing the same hold-down studs/nuts, resulting in high temp variation on the intake manifold. I suspect that if you examine the rearmost attach bolts/nuts, you will find them loose. In my case, the most aft bolt was finger loose. This releases the intake manifold hold-down force, allowing air to get sucked into the manifold past the intake gasket, happily whistling as it does so. Throttle to idle, a-whistling we go.
IF (a big IF) you catch it early enough, you might be able to re-torque those rear manifold attach bolts and save the gasket. In my case, both the intake and exhaust gaskets had already experienced blow-by damage, so tightening did not solve the problem, at least, not for long.
The permanent fix was to remove the intake and exhaust manifolds. Resurface the intake flanges nice and flat. I opted to replace the exhaust manifold. Get new gaskets, reassemble and carefully torque all the bolts in the correct order and torque value. While you have it apart, pay close attention to the cylinder head side at the manifold attachments and make sure that that surface has not been compromised.
A couple other things to consider...
1.) This condition results in the rear cylinder(s) running lean, something you might notice when examining the spark plug(s).
2.) VERY IMPORTANT! When the job is done and you are whistle free, you need to periodically get a long ratchet extension and tighten/re-torque those rearmost manifold retention bolts/nuts. How often depends on your vehicle usage. With newly resurfaced or new parts, the heat/cooling cycle allows those particular bolts/nuts to "work" loose. I checked mine every week or two and found them to be initially loosening, but not leaking. After a couple months, the bolts tended to remain tight... the seating and stretching had "set", if you will. But still after a couple years now, I still periodically go in and check the torque on ALL the manifold bolts.