In your case (with a very high decimation order), linear interpolation may be a good choice, assuming that the bandwidth of your signal is low compared to the input sample rate.
Another idea, if you really need the aliasing rejection that the FIR filter mode offers you AND your sample rate of 1 kHz is "almost" equally sampled, could be to do a two-step process. 1 - Resample your xy data to a waveform sampled at 1 kHz using linear interpolation or spline and then 2 - decimate (resample) the resulting waveform down to 5 Hz using the FIR filter mode. Whether this will work in a satisfactory way for you or not depends a lot on your actual signal, but it may be worth trying.
