Ultimately, the legal check on the President is not the Department of Justice, nor the FBI etc., as these are all arms of the Executive Branch, and so are ultimately under the President's control. The constitutional and legal check on the President is Congress itself. Congress has the power to impeach and investigate the president, and remove him from office.
This is why some people are so adamant about creating a Special Prosecutor: one who is not subject to the President's whims and cannot simply be fired or otherwise intimidated by such, nor is subject to partisan and party-line politics that might influence the Congressional chambers. It's also why the House and Senate investigations are under such intense scrutiny, with any perceived procedural oddities leading to intense and sometimes broadly bipartisan criticism. With continued refusal from Congress to appoint an independent investigation, Congress is the closest thing we've got to an investigative team that can't be intimidated or obstructed by the President (assuming, of course, that he attempts to do so, or already has).
The aforementioned party-line politics makes this questionable, to both sides of the political fence: Republicans seem prone to think the Democrats are on a witch-hunt, while Democrats seem prone to think the Republicans are engaging in a cover-up.