How are cloud bases and tops reported on PIREPS?
It depends. For a PIREP cloud Heights are reported as they are read by the pilot. 

FAR AIM 7-1-16(b)


  ... In reports disseminated as PIREPs, height references are given the same as received from pilots, that is, above MSL.


This means some conditions may be reported MSL as read of the altimeter at local barometer settings while others may be set at standard pressure and read from there. I would assume that altitude reports less than 18,000ft are MSL.