There is no way of knowing for sure because it depends on the software you are trying to run.

If your software is able to use the multiple processors for parallel processing the quad option may well be better. But many apps don't do that, in which case the faster dual processors will have better performance.

Another factor is your workload characteristics. Can you run your software multiple times? For example, I once administered a 24 processor webserver where we ran up to 80 instances of a webserver all at once. The fact that we had lots of processors didn't make any of the individual webservers run faster, but it did allow us to have more running at once without slowing down the box. In a case like that more processors is helpful. But if you are running just a single instance of your app the extra processors are useless (unless the app does parallel threading like I mentinoed above).

Your best option is to install your software on both types and benchmark it before buying if possible.