It seems clear that the FBI and the CIA knew quite a lot about Felix Sater. They worked with him and had him performed services tied to 'national security' for over a decade. It seems quite likely though we don't know for certain that he worked on the CIA's behalf purchasing weapons on the Central Asian and post-Soviet black market in the years when such weapons were easier to come by. If this is true, that also certainly required him to have pretty deep relationships in the post-Soviet criminal underworld and possibly with state actors as well. These specifics we cannot be certain of. What is clear, from Court statements and the federal governments actions is that Sater was performing services which the US government considered very valuable and very secret.
Sater was also clearly dirty. He had been convicted of securities fraud in league with New York City organized crime families. He had been sued multiple times for defrauding investors in other projects. He had also played a key role arranging investments from Russian and post-Soviet sources to fund various Trump enterprises. There are other things which may be true, for which there is a substantial amount of circumstantial evidence. But everything I'm focusing on here rests on very firm foundations.
With someone like Sater you must always leave open the possibility that the reputation is simply the work of an effective self-promoter and con-man. Sater certainly qualifies. But the extreme lengths the federal government went to to conceal Sater's crimes and protect him from punishment makes clear that there was a lot more than talk behind Sater's reputation.
Sater's business relationship with Trump were extensive enough that there's little doubt that his FBI and likely CIA handlers would have had some knowledge of them since he carried on this relationship while working as an FBI/CIA informant and awaiting sentencing - at least from 2003 to 2009 and perhaps going back to 2000.
Trump's longstanding ties to Sater probably wouldn't have mattered much as long as Trump was just a flashy real estate developer and reality TV star. But one can readily imagine that US law enforcement and perhaps intelligence would have become highly concerned once Trump - with his reliance on money from Russian oligarchs and the post-Soviet criminal underworld - started edging his way toward the presidency and especially after he won election on November 8th, 2016.
My point here is that before US law enforcement and intelligence agencies learned about the Russian hacking campaign, received intercepts about communications between Trump advisors and Russian state officials or got hold of that 'dossier' from the former MI6 agent, they may well have had concerns about Trump and the people around him that stemmed from things they learned long before he ever decided to run for President.