I think the following imply that all charges which are a) federal b) capital charges are determined by Grand Jury.
Federal Grand Jury
The Fifth Amendment to the U.S. Constitution requires that federal charges for capital and infamous crimes be brought by a indictment returned by a grand jury.
Grand Jury Clause
The Fifth Amendment to the United States Constitution provides that "No person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a Grand Jury, except in cases arising in the land or naval forces, or in the Militia, when in actual service in time of War or public danger . . . ."
As or difference between "capital charge" and "felony", this reference says,
Currently, federal law permits the trial of misdemeanors without indictments.[6] Additionally, in trials of non-capital felonies, the prosecution may proceed without indictments if the defendants waive their Fifth Amendment right.
I think that implies that grand juries approve all federal felony charges, not just capital charges.
The statistics are found in Table 2.3 on page 12 of Federal Justice Statistics 2010 -
Statistical Tables which says there were 30,000 times when U.S. attorneys declined to prosecute, of which 11 were because the grand jury return "No true bill".
162,350 doesn't appear in that document. It appears to have been calculated by subtracting 30,670 not prosecuted (in Table 2.3) from 193,021 suspects (top of Table 2.2).
Table 4.1 shows that most although not all of these cases were felonies (thus presumably indicted by grand jury per the Fifth Amendment).
I don't understand why Table 4.1 lists a total of 99,921 "cases commenced", instead of 162,000. Still, those numbers are the same order of magnitude: and even 11/99,921 indeed implies 99.99%.
Here are other references saying almost the same thing as the Washington Post,
Rubber stamp for the prosecution
According to the American Bar Association (ABA), the grand jury has come under increasing criticism for being a mere "rubber stamp" for the prosecution without adequate procedural safeguards. ... at the mercy of very well trained and experienced federal prosecutors. Grand jurors often hear only the prosecutor's side of the case and are usually persuaded by them. Grand juries almost always indict people on the prosecutor's recommendation.[48] A chief judge of New York State’s highest court, Sol Wachtler, once said that grand juries were so pliable that a prosecutor could get a grand jury to “indict a ham sandwich.”[49] And William J. Campbell, a former federal district judge in Chicago, noted: “[T]oday, the grand jury is the total captive of the prosecutor who, if he is candid, will concede that he can indict anybody, at any time, for almost anything, before any grand jury.”[50]
