The obvious answer to me is John Wolyniec, with Luke Rodgers behind him.
I was in elementary school during the early days of MLS, so I had literally never heard of Rhett Harty until I read this.
Woly also holds the stats of being the only one to ever score an MLS cup final goal for us. Shame we didn't even get to celebrate it for long since Columbus scored like 90 seconds later.