I know the U shape clips comes off but it does not budge. I'm afraid of breaking it. I've done an extensive search and can't figure it out. What tool do I use? This is a pic from the internet but mines a 1st gen 4Runner:

 

flat head screwdriver and pry upwards from inside the U... might help to turn it a little so it has room to pop out... good luck

 

Is the clip rusted into place?

In the past, I have just taken a pair of pliers and just pulled these types of clips free. However, I have only done this with license plate lights in an aftermarket bumper so the spring force wasn't very strong.

All I can think of is letting it soak in penetrating oil and try to get the clip to rotate a little before pulling it off.

 

On the picture above, I put a flat blade against the top of the clip and push it in an upward motion. It is just held in place by pressure of the bent tabs. Sometimes a good thump with the heel of your hand on the screw driver is needed. Make sure it is not corroded to the door but it is most likely the pressure holding the clip.

 

Like everyone else says.

The good news is that the clip is VERY standard. If you break yours, any locksmith will have a box of replacements.

 

Spray penetrating lube of your choice will work wonders

Those clips are spring steel they might bend I have never had one break .

Even beating one off with a hammer and Chisel

 

Yes, yes and yes.