FMC run for GFCI receptacle?
Nec Article 348 allows FMC to be used as a conduit system. However, NEC 348.12 (1) does not permit the use of FMC in wet locations. So assuming you water heater room is not wet during normal operations FMC can be used. However, if you determine that the wiring might cause a shock or burn hazard during non-normal working conditions some AHJ might have a problem with it. 

Due to the fact that this is probably a short run and so material cost would not be a real factor, I would suggest you run it in LFNC "carflex" or LFMC "sealtite" and avoid any conflict.