I think this is a very difficult question to answer, not least because
1. The sample size is small
2. Without having had multiple TOCs running the same route, how do you know how good a job they've done? (or for those more statistically minded, this is just point 1 made again).
Most people have said Chiltern. Well, they've been the only TOC to run the Chiltern Mainline, a line which had, for the most part, been resigned to the rump of the railways by BR. They were given an experimental "long" franchise, much longer than any of the others, simply because at original franchising, no-one would get a decent return on investment otherwise. They have done a decent job, but we don't know what anyone else would have done.
Certainly the claims of "Anglia Railways", are very interesting, because that's been a service run by 3 different railway companies and for one to be better than the others is actually notable, although again, that is a distinction between a TOC who's only responsibility was an Inter City mainline and some regional services, and one who's had to deal with a host of commuter services, an intercity mainline and an airport express.
Various East Coast mainline companies (except Virgin) have also been mentioned, which probably just reflects the general high standard of East Coast Mainline services.
Also notable is that the Southern and Southeastern TOCs have also been put down as some of the worst. Notably, they run an unbelievable number of commuter services across some horrible networks (high frequency across flat junctions, lots of alternative routes, all of whom want their turn-up-and-go to multiple termini). Again, that is far more indicative of the network they have to run than the performance of the TOC.