I have a 97 4runner with 109,000 miles. The antenna will not go up and down, but the motor is running and grinding. Should I replace the antenna motor, or disconnect the motor? If I just disconnect the motor, will it also disconnect the radio?

It's probably the mast, not the rotor. You can disconnect the motor, the harness should be under the pass side front fender. Won't hurt anything.

yup, sounds like the mast is broken. from what i've heard, a lot of people have had the same prob- including me. Why don't you replace the mast? It's a bit expensive at the dealership (labor is more expensive than the mast itself) , so i recommend taking it somewhere else.

Interesting idea:
http://www.toyotanation.com/forum/t65507.html

you can buy a mast cheap on the internet, very easy to install