Do PNP transistors have low noise?
I am very sure that the noise generated by holes and electrons is quite the same. If there are differences in the NPN and PNP transistor, they must be an indirect cause and not caused by the type of carriers.

Essentially there are only two dominant types of (white) noise sources

1) shot noise (this is due to the discreteness of carrier flow when passing a potential barrier such as a PN junction). 
This is independent on the device structure, doping levels, material compostition, carrier type and so on. It is fundamental and the same for holes and electrons (independent on temperature, only depends on current!).

2) thermal or resisitive noise (due to brownian motion of carriers in a resisitive layers)
This is also fundamental and only depends on temperature and overall resistance.

Hence transisitors, having e.g. different layer resistances will also generate different amount of noise. This may be the cause for different behavior of PNP and NPN transisors (or more precisely, between any pair of transistors, not just different polarity). Shot noise is quite the same in all bipolar transistors.

BTW: The noise generated by surface states (as mentioned by rawbrawb) is always some kind of 1/f noise and vanishes at a certain frequency (in contrast to the above two white noise sources). Contrary to white noise (which is quite easily explained) 1/f noise is a vrey complicated phenomenon with many different effects that can cause it. It strongly depends on material quality, device strucure and so on. 
Strong differences between devices are expected for 1/f noise. So always look for the frequency the noise is specified at!