Yes, the Y. Pestis (the bubonic plague disease) was worse than necrotizing fasciitis, because the bubonic plague killed many more people. The bubonic plague was incredibly deadly for those it hit, and treatment was not really an option, so the death rate was very high. The bubonic plague has been a much bigger problem, historically.
While no one would want to have either disease, and both would likely be equally painful in their symptoms, necrotizing fasciitis is not easily passed or contracted. This makes the bubonic plague more of a threat and a worse disease, since it is passed typically by fleas. This disease can spread much more quickly and is far more contagious. Because of the way in which each disease is spread, bubonic plague would be far worse for the population overall, effecting more people and causing more deaths.