Guys, I'm happy to report that the issue has been resolved. If you have the same issue as I did, make sure you buy the high quality OEM antenna mast. They are only a few bucks difference, made my day.
Here is the ebay seller I bought from which DID NOT work.
eBay - New & used electronics, cars, apparel, collectibles, sporting goods & more at low prices
Here is the ebay seller I bought from DID work.
eBay - New & used electronics, cars, apparel, collectibles, sporting goods & more at low prices
Both of them claimed their antenna masts work on 99 4Runner but the quality is totally different. More importantly, the real OEM mast is a little bit thicker than the after market one.
Buy the real Toyota antenna masts, they are about $45 shipped on ebay. Don't buy the cheap ones. The cheap one goes down right but the motor would keep on pushing even though it is all the way up. I replaced it with the real Toyota antenna and it worked perfect.