Which Board Should I Use For High Frequency GPS?
Any single board computer will be able to run an averaging decimating filter at 50 samples per second, even if using a high level interpreted scripting language. Even the apollo guidance computer would have been able to do that 50 years ago. But ...  averaging NMEA-coordinates will not enhance accuracy.

First a little bit of hair splitting: Accuracy is the absence of a systematic error or bias, averaging will not help with this. Precision, the absence of random errors, is what you are after.

Second: You are doing signal processing. Understanding filter-theory will help with this issue. Really. Stephen W. Smith's book on DSP is a good introduction. 

Third: 40 NMEA-coordinates per second are the output of some (interpolating) filter. In the design of this filter, there is a tradeoff between maximum trackable dynamics (in \$m/s^2\$) and precision. The tradeoff may be affected by the selected update rate. When you set the chip to 1 update per second, it may apply far better filtering than you may be able to do (altering integration period, carrier/code-tracking loop filters etc.)