I guess their size is very small so you can perform EDX using 5 kV for qualitative analysis, but the best method is TEM with FIB sample preparation.

Neutron diffraction

Boron is quite challenging for EDX so that I would recommend diffraction techniques. Although I am working for many years with Ni-base superalloys I never came in touch with them. in so far I would be surprized that there are many borides  in this material. Therefore any integrating diffraction technique like y-ray and neutron diffrcation I would  exclude. I would take local techniques like TEM (quite time expensive and costy) or better EBSD into account. The existence of boron you can evaluate using BSE contrast. This has a much better resolution than EDX and BSE does not have any energy resolution limit, i.e. you will see them as dark particle in a very bright matrix. Which boride should become clear using electron diffraction (EBSD).

I would suggest you try extracting minor precipitate from matrix by electrolytic route. You can look over a proper eletrolite solution (look at handbook of metallographic preparation ASM) that reacts, selectively, dissolving only the matrix Ni(ss). After that, you collect the solution, filter, dry, and take the "residual" material and analyze using SEM and/or x-ray diffraction to characterize it. I did it and worked fine.

Read this paper: 

Article Thermodynamic Evaluation of the Phase Stability and Microstr...

TEM - EDS line scans across inter-granular particles would indicates Mo or Mo - Cr rich phase. SADPs of these particles from different zone axis will confirm if the particle is FCC carbide of BCT Boride.