No, there weren't any "boos" -- that was the traditional greeting of "Bruuuce!" New York Daily News:

The most popular New Jersey export took a moment to chime in on his state's current events with song — and he did it with a little help from Jimmy Fallon.
Bruce Springsteen stopped by "Late Night" on Tuesday night, and joined the comedian in a reworked version of his song "Born to Run," spoofing the Fort Lee, N.J., bridge scandal currently plaguing Gov. Chris Christie.

The new song, titled "Gov. Christie Traffic Jam," started with Fallon — dressed as Springsteen — singing about being stuck on the George Washington Bridge for hours. He was soon joined by the real Boss.
"You've got Wall Street masters stuck cheek-to-cheek with blue-collar truckers," the legendary rocker, 64, sang. "And I really gotta take a leak."

In true Springsteen fashion, the funny address to Christie frequently referenced the "working man."
By the end of their parody, Fallon and Springsteen had the audience laughing and cheering, but maybe not everybody shared the sentiment on the "Bridgegate" scandal — towards the end, it sounded like they may have garnered a few boos.

H/t Nicole Sandler.