I think you'll find that you'll get good performance either way. .NET compiles into an intermediate code (IL), which is then compiled into x86 when you run the program (a process known as JIT, or Just In Time, compiling).
LabVIEW compiles it's VI's directly into x86 code. But really they are both fast solutions.
I think the difference comes down to preference for your case. Many people, especially on this forum, would say that you can get the code written much faster in LabVIEW (and your application is a classic type that LV is designed to do well). But, if you've programmed in VB or C all your life, you might find .NET easier.