Jordan was probably the best in-game dunker. As far as dunk contests, the MJ/Dominique contests were a little before my time but I will say Vince's performance in the 2000 dunk contest was the greatest dunking performance I've ever seen - because the hype leading up to that event was off the charts (dunk contest had taken a 2 year hiatis) and Vince not only lived up to the hype - he exceeded everyone's expectations.
MJ, Dominique, Dr. J, Vince...really no right answer but those guys are at the top of the list for me.