If starting from scratch, I'd take the Jeep over the VW.
That being said, you aren't starting from scratch. If you think buying a 14 year old Jeep with an unknown maintenance history and 125k miles is going to get you a more reliable vehicle, I wish you luck. Parts will be cheaper, and repair work is generally pretty simple on these with tons of aftermarket support if you choose to tackle it yourself.
I say that as a former owner of a Cherokee. ( I was on my 3rd water pump at 135,00 miles). Fun for what it was, a tank in the snow, etc... but reliable was a touch of stretch - it was reliable so long as you kept up with the nickel and dime stuff and wrenched on it yourself. It would also run forever! No doubt the 4.0 is a decent engine - its all the stuff bolted to it that will get you!