They knew but to prosecute would take the onus off of the “White, Christian, Right Wing Militias”.
The Clinton Administration wanted no part of a war against international Islamic terrorism.
They turned down capture of OBL. They did little in response to the Kobar Towers destruction, The USS Cole destruction, et al.
The 9-11 attack was in the planning since 1998 stateside and the plot to fly planes into buildings was discovered even before that (and may have ties to the OKC bombing).
McVeigh and Nichols were guilty, no denying that. But the administration wanted to cut the investigation to a few names. Even other participants names aren’t so widely known (household names) as they gave up testimony for lighter sentences. Guilt is guilt, while make bargains with terrorists for testimony?