To me, it ALL depends on the quality of the swap.
If you get someone who hack their way through it, and you know that they're out there, then I'd rather have the 7M. Every time. It's way harder to fix bad work than it is to start over and do good work.
There's also the way that it's been treated, but you can't control that. I see way too many JZ swaps motivated by poor maintenance, so to me, the JZ swap is something of a red flag. Different if it's a JZA70 to start with, of course. I'd be VERY careful about inspecting the general condition of the car with the JZ swap, even more so than I would be about the 7M. (Not that I'd be lax with either. It's a 20+ year old sports car, I expect some hard mileage on them.)
All that said, we all know that even if the swap costs $4k, it doesn't add $4k to the value of the vehicle. If you were going to swap to JZ anyway, and the work done is good, then it's a no-brainer to go with the JZ swapped car. If, on the other hand, you want to be able to take the car to a shop and just tell them to change the timing belt, or some other task without having to go through the car's life story, then the 7M becomes a more obvious choice.