It really depends on what you consider the modern era. Ed Walsh, who pitched for the Chicago White Sox from 1904-1917 has the lowest all-time ERA at 1.82. he pitched 2,969.1 innings. Carl Hubbell, who pitched for the New York Giants from 1928-1945 has a career ERA of 2.97 in 3,589.1 innings pitched. However, Hoyt Wilhelm, who pitched for 10 teams from 1952-1972 has an ERA of 2.52 in 2,254 innings. So, if you consider the modern area to begin after 1920 (as most peopel do), then Wilhelm is your guy. Pedro Martinez and Greg Mddux are the top two active ERAs in my lifetime.

Here's all the pitchers since 1900 that had an ERA under 3.00 that pitched at least 2000 innings. ---------------ERA IP 1 Ed Walsh 1.82 2965 2 Addie Joss 1.89 2327.1 3 Three Finger Brown 2.06 3172.1 4 Rube Waddell 2.13 2868.1 5 Christy Mathewson 2.13 4780.1 6 Walter Johnson 2.17 5914.2 7 Cy Young 2.19 3634.1 8 Ed Reulbach 2.28 2633 9 Eddie Plank 2.35 4495.2 10 Sam Leever 2.35 2248.2 11 Eddie Cicotte 2.37 3223 12 Doc White 2.39 3040.2 13 Nap Rucker 2.42 2375.1 14 Chief Bender 2.45 3018 15 Hooks Wiltse 2.47 2111 16 Hippo Vaughn 2.49 2730.1 17 Bob Ewing 2.49 2301.2 18 Jack Taylor 2.50 2220 19 Deacon Phillippe 2.50 2286.2 20 Hoyt Wilhelm 2.52 2253 21 Grover C Alexander 2.56 5189 22 Slim Sallee 2.57 2821 23 Frank Smith 2.59 2273 24 Jack Chesbro 2.61 2747.2 25 Harry Howell 2.62 2340.1 26 Vic Willis 2.62 3343.1 27 Wild Bill Donovan 2.63 2851.2 28 Red Ames 2.63 3197 29 Claude Hendrix 2.65 2372 30 Joe McGinnity 2.65 3074.2 31 Dick Rudolph 2.66 2048 32 Tully Sparks 2.68 2158.1 33 Cy Falkenberg 2.68 2275.1 34 Fred Toney 2.69 2206 35 Pedro Martinez 2.72 2513 36 Whitey Ford 2.74 3171 37 Babe Adams 2.75 2994.2 38 Howie Camnitz 2.75 2086 39 Sandy Koufax 2.76 2325 40 Dutch Leonard 2.76 2192 41 Jeff Pfeffer 2.77 2408.1 42 Earl Moore 2.78 2775.2 43 Jack Coombs 2.78 2320.2 44 George Mullin 2.82 3686.2 45 Bill Dinneen 2.82 2566 46 Jim Palmer 2.86 3948 47 Andy Messersmith 2.86 2229.2 48 Tom Seaver 2.86 4782.2 49 Stan Coveleski 2.88 3093 50 Juan Marichal 2.89 3506 51 Wilbur Cooper 2.89 3482 52 Jack Powell 2.90 3448 53 Bob Gibson 2.91 3885 54 Carl Mays 2.92 3020.2 55 Dean Chance 2.92 2148 56 Don Drysdale 2.95 3432 57 Lefty Tyler 2.95 2228 58 Mel Stottlemyre 2.97 2662 59 Bill Doak 2.98 2782 60 Carl Hubbell 2.98 3591