First NFL season he threw 6 TD's, 9 INT's, 48%, 55 QB rating
Second season he threw 24 TD's, 17 INT's, 52%, 75 QB rating
Alex Smith threw 50% completion in his first year, and second year threw 58% and had a 74 QB rating. So the two are very comparable, but Alex Smith thus far has been more accurate than Eli Manning has his whole career.
EDIT: Also, Eli Manning's supporting cast is miles better than Alex Smith's.