Let's compare the two, shall we?
Rookie year (2004)
Roethlisberger - 17 Touchdowns 11 Interceptions
Manning - 6 Touchdowns 9 Interceptions
2005
Roethlisberger - 17 Touchdowns 9 Interceptions
Manning - 24 Touchdowns 17 Interceptions
2006
Roethlisberger - 18 Touchdowns 23 Interceptions
Manning - 24 Touchdowns 18 Interceptions
2007
Roethlisberger - 32 Touchdowns 11 Interceptions
Manning - 23 Touchdowns 20 Interceptions
2008
Roethlisberger - 17 Touchdowns 14 Interceptions
Manning - 21 Touchdowns 10 Interceptions
Career Totals
Roethlisberger - 101 Touchdowns 68 Interceptions
Manning - 98 Touchdowns 74 Interceptions
When comparing them, you have to take into consideration that the Steelers were a run first team up until this season. Whereas the Giants have been pass oriented, even with Tiki "I fumble too much" Barber. Both have a Super Bowl win. Eli has a Super Bowl MVP that was a total joke, as it should have went to Tuck, easily, so that point is completely moot.
Also, factor in Ben's big play ability, and his ability to get away from the pass rush. He has 10 career rushing Touchdowns to Eli's 3. Eli's had one of the best offensive line's in football in front of him this year. Ben's had one of the worst once you factor in injuries. Not to mention the lack of the running game on the Steelers at the moment.
Thus, Roethlisberger > Manning all day, everyday, and twice on Sundays.