A reply I wrote just before the boards went offline. May be some double coverage here, but I'm too lazy to fix. :p
He could zap out the tires, but that would send it spinning out of control.
He could put obstacles in its path to slow it down or force the driver to stop. Dump a big pile of mud, say, in front of it.
He could use his super breath, which has been shown to be powerful enough to push cars around.
He could use his heat vision to zap something in the engine. One of the gears or belts or wires crucial to making it go. (Fuel line not recommended.)
Similarly (although more difficult to pull off for a variety of reasons), he could use his freeze breath to freeze the engine block.
He could use his freeze breath to freeze the road. Car would lose traction (and also control), but if he had something to cushion the impact...
A little more crazy, but... he could build a ramp and put it down in front of the car. Don't know if he's allowed to catch it in mid-air or if he could use something to catch it or if there's a soft landing place available or something.
Back to obstacles... He could fly to New York, grab Spider-Man, fly back, and have him build a web...
(Or, you know, find some flexible cargo netting and use that. Like the netting they use on aircraft carriers for emergency landings. There might be something of the sort lying around at the naval base which is no doubt located somewhere in harbor area...)
Note that some or all of these options could affect other cars in the area, depending on conditions.