What was supposed to be a memorable climax to the club's 112 years at the stadium in east London turned ugly before kick-off on Tuesday, and newspaper back pages on Wednesday were dominated by images of United's coach with several windows shattered.
Video footage filmed inside the coach by United's players went viral on social media, while TV footage of the violence was shown around the world.
West Ham's co-chairman David Sullivan and vice-chairman Karren Brady condemned those who marred a historic night and apologised to United's players and staff.
"Sadly, the actions of very small minority of people outside the ground prior to kick-off risks overshadowing those celebrations," Sullivan told West Ham's website (www.whufc.com).
"I want to be clear -- their behaviour was completely unacceptable and does not represent our club or our values."
Speaking to Sky Sports on Tuesday, Sullivan had initially seemed unaware of the seriousness of the incidents and blamed Manchester United for causing a 45-minute delay to the game, the last to be played at the Boleyn Ground.
"When I was asked about the incident prior to yesterday's game, I was unaware of the damage that had occurred to the Manchester United team bus," he said on Wednesday.
"I want to apologise to Manchester United for that damage and assure them that we will be doing all we can to track down those responsible and ban them for life."
On Twitter, Brady defended West Ham as a family club and said the vast majority of fans had attended Tuesday's final game "to respectfully say Farewell Boleyn".
LIFE BANS
"Those who chose to behave unacceptably will be dealt with in the strongest way possible, with life bans for those guilty of violence," she added.
West Ham have played at the 35,000-capacity Boleyn Ground since 1904 but will move next season to the 700 million pound Olympic Stadium after agreeing a 99-year lease.
Thousands of fans had swarmed the streets around the stadium in Upton Park on Tuesday, many without tickets for the game.
United's coach came under attack as it passed a statue of West Ham's former England captain Bobby Moore, posing with the 1966 World Cup.
One officer from London's Metropolitan Police and a member of the public sustained minor injuries. No arrests were made.
The Football Association announced that it would launch a full investigation of the incidents, including objects being thrown at United goalkeeper David de Gea during the game.
On the field, West Ham's 3-2 win over United provided a fitting finale, before an after-match show that heralded a new era for the club as it moves to its new ground three miles away in Stratford.
(Editing by Catherine Evans)
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