I have the same thing, but I'm going with Cotchery, and here's why:
1)Indy has allowed other teams to throw on them, when the quaterback wasn't a complete waste (I'm not saying Leftwich was terrible, but he was abysmally bad ) Eli had 247 and 2 TD passes; David Carr went 22/26 with 3.
2) McNair is really ugly looking this year. Like, really, really ugly. They escaped Cleveland thanks mostly to Chaz Frye goofing terribly, a good defense (increasingly banged up) and Stover being money. As much as I hate saying this, Cotchery has a better QB.
3) Yes, SD hasn't played anybody, but I'm not convinced that Indy's schedule to date is as much as we thought it could be. So I don't think you get to ignore the fact that SD's pass defense comes so highly rated, particularly with the washed up QB factor.
4) Cotchery is close to being my man crush for 2006 fantasy purposes.
I'm sure I'm waaaaaaay in the minority on this, but them's my thoughts. Good luck either way: hopefully they both go off, and you and I can rest happy either way.