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The #7 train (which would be the answer to the question even if you didn't specify rush hour!) The Lexington Avenue line (4, 5, 6 trains) comes in second. And you might not think so at first, but the L line gets strong consideration for third place. Trust the former conductor when I tell you this.
I think the #1 train coming from Uptown is up there on the list. It gets so crowded sometimes that they can't even let anyone on for a few trains. It is most annoying. I avoid this train like the plague.
The E & 6 train gets pretty packed during rush hour.
I used to take the L and didn't think it was as bad as the E or 6. One thing I will save about the L, is that is FLIES through the tunnels going into/out of the city and brooklyn! Actually can get kinda scary sometimes....
I've heard the stat that the Lexington Avenue Line trains (4/5/6 together) move more people each morning than any entire transit system in the US... like the 4/5/6 has higher ridership than the whole DC Metro, Chicago Ls, Boston T, etc... a pretty amazing indicator.
4/5 train def, I don't think the 6 train is miserable at all, actually I consider the 6 train to be the most reliable/comfortable of all the trains. The 2 train is very busy as well, even on weekends.
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