I happen to think they were both great generals.
I don't agree with Lee detractors like Connally. His defensive war during the Overland Campaign of May-July 1864 was nothing short of brilliant: anticipating Grant's every move, always matching him in the nick of time, despite the depletion of his officer corps, generally erratic corps commanders, inferior numbers, and a weakening cavalry arm and terrible logistic support from Richmond. Lee had a couple of bad days at Gettysburg, some very bad luck before Antietam and tended at times to place too much trust in questionable senior commanders. But on the whole, his record at the head of the ANV is magnificent. Not overrated.
The knock against Grant...we all know. Superior numbers and logistics, attrition, yadda yaddda yadda. To which I respond: His Vicksburg campaign is considered by many experts to be the most brilliant single offensive campaign of the entire war - yet it's largely forgotten because it wasn't in Virginia. Let us not forget that before Lincoln called Grant East, he had managed the surrender of two entire Confederate field armies and had chased a third clean over the horizon. Grant's effectiveness in Virginia was hampered by being saddled with some incompetent (Butler, Burnside, Ledlie) and lacadaisacal (Smith, Warren) commanders that he didn't have to put up with out West. Opportunities to destroy Lee were repeatedly cast away by bungling by various commanders in 1864. Only Cold Harbor stands out for criticism, both for the assault and also Grant's refusal to ask for a truce to retrieve his wounded.
I'd round out my Civil War Top Five with Jackson, Forrest, and maybe a tossup between Gordon, Sheridan, Longstreet, Jo Shelby and Richard Taylor for the last spot.
Beyond that I'd like to single out Subedei, chief general of Batu Khan during his invasion of Russia and Europe in the 1240's, as one too often overlooked. His campaign essentially conquered a third of Eurasia in just a few years time.
For his destruction of the Army of the Tennessee (at Nashville), I'd nominate George H. Thomas.