I think it's mainly because 99% of QFT research in the last fifty years was on perturbation theory, and you can only do perturbation theory in momentum basis. In a free theory, eigenstates of momentum evolve with time in a very simple manner (a particle with momentum p remains a particle with momentum p, evolve it and you just get a multiplicative phase), whereas eigenstates of position are messy (you start with a particle localized in point x, you evolve the system, and you get a complex superposition of particles localized in all points inside x's future light cone, and some particles outside it). If you perturb about that free theory, you get small probabilities for momentum eigenstates to interact and become different momentum eigenstates, which are, to the first order in coupling constant, just Feynman tree diagrams. You can't simplify the theory like that in position basis.
You can easily convert between one and the other (it's just a linear transformation), but position operators just happen to be much less useful for everyday computations.
Now, of course, once you get into strongly coupled scenarios such as lattice QCD, tables are turned and position basis suddenly becomes interesting. And if you want to quantize gravity, you can't (or shouldn't) do that in momentum basis either, because real physics is local and momentum basis is inherently not - it just happens to work because we assume in regular QFT that spacetime is Minkowski. If you want to do quantum gravity (seriously - not just an IR approximation), Minkowskianness, Fourier transforms, etc. all go out the window and you're forced to do quantum field theory in a way that's counter to all your training.
There are some interesting aspects of QFT in position basis, such as Feynman checkerboard, polymer model of fermions, ... But overall I don't think that area is all that heavily researched.