How do historians reconcile the historic record with the media manipulation that it would be IMHO naive to say did not exist before the current political era?

Obviously this is going to be an issue when you use any source, because bias is inherent in just about every form of documentation produced by people.

I use newspapers a lot in my work. Specifically, I'm interested in how people represented themselves professionally in the media (newspapers, mostly, but also self-published monographs and pamphlets). When I'm using newspapers, I'm always cognizant of their value as historical record. It's probably easiest if I break that value down into several key points.

(1) Factual value - If a newspaper article states that something happened (eg. an institution opened, a man was murdered, a political actor made such and such a statement) the first thing I will do is look at other newspapers from the same date and maybe about a week after. If all newspaper agree to the fundamentals of that story, regardless of their political bias (which I also have in mind), it is probably safe to say that it happened as reported. Usually, if someone disagreed with any aspect of the story, it would come out in a rival paper or an editorial. If that's the case, the next step is to reconcile that new wrinkle with the event as represented initially. It can be a long and arduous process.

(2) Insight into public opinion - Even if I'm not interested in using a newspaper to piece together historical "fact," I'm very interested in how they reflect public opinion. Newspapers in the nineteenth-century, as now, would print stories that they believed people would be interested in reading. They can be used as something of a barometer of public interest in a given subject. However, they could also be used to push an agenda, regardless of public interest in said agenda. That's where cross-referencing between papers again becomes valuable. Paper A (a conservative organ) may publish an article about Joe Blow, a politician. Paper B (a liberal organ) may then publish a counter-argument, claiming that Paper A's claims about Joe Blow are hyperbolic, and that not as many people support him as Paper A claims, or something to that effect. Neither paper can be trusted, but the argument around Joe Blow obviously garnered enough interest to merit a public debate. Editorials would illuminate further interest from readers or other political actors.

(3) How papers were actively used to push an agenda - In my own research, and in a lot of other research I have read, there is a great deal of interest in how people felt they could use a paper to push their agenda. An editor who writes a slurry of articles about a certain political or public policy issue obviously feels there is some benefit in doing so. I, as a historian, have to ask: why? Why does he feel this venue is appropriate to utilise as a mouthpiece for his cause? Thus, papers become valuable in the sense that they are just another public venue for discussion, and we can gain great insight into someone's motivations by asking why they chose to represent themselves and their cause in the pages of a paper. The manner in which they do so (their rhetoric) also gives us insight into their motivations.

So to sum it up, I think most historians have always been aware of the inherent biases of the media, and those biases (manipulation, as you phrased it) actually figure very prominently into historical methodology and theory.