Goals from Karl Bermingham and Paul Murphy set City on their way to a 2-0 victory and a semi-final clash with Charlton Athletic, after Hammers had been unable to breach a defence which, in games against Wrexham, Peterborough and Millwall along the way, had not conceded a goal.
But Tony was magnanimous in defeat and says: "We were under sustained pressure and we couldn't get the ball out of our half, to be honest, at that period of the game.
"They ended up punishing us on the hour before getting the second 10 minutes later while they were having a real spell when they were on top.
"We cleared a corner, they crossed it back again, we were appealing vainly for offside but their fellow headed it in at the back post.
"Our boys were adamant - but it was not to be.
"But it was fair and square. I have to hold my hand up and say they were the better team.
"Our boys worked ever so hard, with George Sealey making a couple of terrific saves in the first half, and another in the second when it was still 0-0.
"We worked very hard but were on the back foot most of the time and the bottom line is we just didn't have the quality.
"We couldn't fault the effort, the commitment, or the desire, but against a very good side we just lacked that little bit of quality to undo them.
"It is not a worry; sometimes you will come across a team that will probably go on and win the tournament.
"We beat Coventry in the final a few years ago and their goalkeeper who let in nine goals over the two legs ended up a top class goalkeeper for Liverpool, Chris Kirkland.
"So as long as we get one or two players from this team and we learn from it - because they had better players generally - you can't complain.
"They are a very, very good team, and there aren't many I could say that about at this level - they'd be the favourites for the competition now."
As for the plus points, Tony says: "The positives were that defensively we played very well because were under constant bombardment. Anton Ferdinand and Elliot Ward did very well, as did George Sealey, but we just lacked a little bit of quality up front and in midfield.
"They were just too good for us in the end and we didn't have enough to hurt them - but we have done very well to get to the last eight of the competition and it is no disgrace to lose to a team like that.
"So while I am disappointed, I am fairly philosophical about it, and I understand that on the night they were the better team."
Team: George Sealey, Tommy Laws, Anton Ferdinand, Elliott Ward, Brent Tattam (Mark Noble 75), Trent McClenahan (Marce Collington 75), Graeme Carrick, Phil Lumsden, Mitchell Cole, Danny Morris (Darren Blewitt 20), Greg Pearson. Subs unused: Matthew Reed (GK), Sam Wright.
Attendance: 1,645