There'll be an element of taste in there- the Jaguar having a Precision pickup will give you a very different sound to the two Jazz pickups in the Fender.
I'd suggest trying both, or at least trying basses with a P-J and two Jazz pick up combinations, to work out the sound you're going for. I have recorded with the Jaguar before and it sounded good, although I wasn't going direct.
For the price of the Fender, you could buy a used VM Jaguar and a VM Jazz. That would give you the best of both, at least.