I had the same issue with an 05 King Ranch. I had a K&N cold air intake when I bought her. I dislike K&N air filters. My take on them is if your letting more airflow in, more **** is going to get in too! Anyhow, I went by a local junkyard and picked up a stock air intake tube and air cleaner box for about $70. Cleaned it up and installed it with a regular air filter and the whistle is GONE GONE!
The whistle I had was drivers side, high pitched, and happened whether it was cold, hot, raining, etc. Happened from about 1500-2000 rpm. It was definitely the K&N CAI!