Bringing out-of-warranty car to the dealership for repair vs. an independent repair shop?

I currently own a 2001 Toyota Avalon with about 140,000 miles on it.

A few months ago, I brought it to Toyota for a routine checkup, and they said they needed to do about $2000 in repairs (something to do with gas leaking?)

Last week, my car was vandalized. A hose connected to my radiator was cut. After driving about 50 miles (before anything bad happened,) my car starts producing smoke from under the hood. Luckily, it happened when I was at a Wendy's drive-thru window and not when I was actually driving. Toyota charges us just under $900.

The question: Am I being screwed? Would a local, independent auto repair shop likely get the same job done for much less?