'36 5W quarter window water seal

[Steve in Denver]

On my '36 5 window, there is rust just above the running board, right below the quarter window. In talking with someone else, he said it was a common problem with the window leaking.

Sooo… what is the best sealant to put around those windows? I don't want to go to the local glass shop because the stuff they use is heated and designed to never come off unless it is cut off. Do I want the 3M sealant or a Home Depot clear silicone? Or is there something better.