Okay, so your post is kind of confused and there's a lot of issues to unpack.
First, the indictment issued friday has nothing to do with collusion. Special Counsel Robert Mueller is not merely investigating whether anyone in the Trump campaign colluded with Russia but also the underlying crime itself: the Russian interference in the election. This indictment, like the previous one, deals with Russian interference and not collusion.
Second, neither the intelligence agencies, nor Mueller, has said that Trump colluded with Russia. We don't know yet whether he did or not. Mueller will issue a report on that issue sometime in the future.
Third, the evidence for Russian interference is in the indictment. You can read it yourself. There's been a lot of reporting about the various evidence which we have for Russian interference. For example, we know from metadata that some of the stolen documents were run through an English-to-Russian translation program and back again. The stolen documents were also opened on machines with cryllic language settings (the alphabet used in Russia). The software and IP addresses used in the attack were the same as ones used in other attacks attributed to Russia. There's a bunch of other evidence that can be pointed to and the case is really ironclad.
Fourth, so it's not just rhe "word" of these intelligence agencies. There's evidence. You also have private cybersecurity firms who have confirmed that it's the Russians as well as journalists who discovered evidence it was the Russians. For example, the AP found a bunch of links which the hackers had used in their spearphishing campaign and who those links had targeted. The targets, which include Europeans, Americans, and anti-Putin activists, seem to have nothing in common but their being enemies of the Russian government.
Fifth, the law does apply to these agencies. They have to follow the law. By issuing this indictment, Robert Mueller and his team are asserting as true the facts contained therein. Lying about them would be a crime and there would be no motive.
Sixth, it's certainly true that Peter Strzock had a lot of ill feelings towards Trump. But this doesn't mean what you think it means. Everyone has political opinions, but that doesn't mean that they can't do their job. Would you argue that a Republican FBI couldnt investigate alleged crimes committed by Hillary Clinton? Moreover, Strzock didn't run this investigation. The indictments were issued by Robert Mueller and his team. So Strzock's bias isn't determinative. Finally, he's not the only one with bias. Trump obviously has bias and has an incredibly strong incentive to lie. So why would we believe anything Trump says about this issue, especially since he has already been caught lying about it before?