[danso]

Watergate is the obvious example. But there haven't been many investigations of presidents – or at least investigations of presidents personally, which seems to be the scope you're asking about. The AP won the 1999 Feature Photography award for its work covering the Lewinsky affair and impeachment hearings [0]. I don't know if I would count Maureen Dowd's award in commentary [1] as specifically challenging the administration. And I think it's arguable that the Clintons' Whitewater controversy had the same amount of "matter" as what President Trump is currently under investigation for, considering Ken Starr's Whitewater probe recommended impeachment for things not directly related to Whitewater (I would agree that Bill Clinton, however, did not get the scrutiny he deserved for Paula Jones and others).

If you expand the scope of "investigation against a president" to include the actions of his administration, then you'll find more examples:

1987 National Reporting Award for the Miami Herald's reporting on Iran-Contra (Bob Woodward of the WaPo was also a finalist on the same topic in this category) [2]

2011 Editorial Writing to the WSJ for its editorials challenging Obamacare [3]

2014 Public Service Award to The Guardian and the WaPo for the Snowden revelations [4]

[0] https://www.pulitzer.org/winners/photo-staff-0

[1] https://www.pulitzer.org/winners/maureen-dowd

[2] https://www.pulitzer.org/winners/staff-21

[3] https://www.pulitzer.org/winners/joseph-rago

[4] https://www.pulitzer.org/winners/guardian-us