The Old Trafford boss caused controversy by contrasting the clubs and describing the Magpies as "a wee club in the North-East" after clashing with their manager Alan Pardew following United's recent 4-3 Premier League victory.
And while he believes Pardew's side should have been competing for trophies more regularly over the years, Sir Alex praised the club's fans as "up there with the best in the game."
| NEWCASTLE LATEST
|33/1||Newcastle are 33/1 with William Hill to win the Europa League this season
"They are up there with the best supporters in the game. Their passion, commitment and fervour have never wavered, even though they have had little to celebrate.
"Sadly, results have not matched their loyalty. If Newcastle's achievements had matched the support of the people who pay to watch them play, the club would be among the game's giants.
"It's tragic that they haven't been able to win a league title for over eighty years."
And rather than offend Newcastle's fans, Sir Alex is seeking to start afresh, and suggests the club's supporters are one of the reasons travelling to St James' Park has been difficult in the past.
"I want to clear up any misunderstanding that may have arisen over what I said. I have nothing but the highest regard for Newcastle fans and I always have had.
"They have turned up in numbers to get behind their team wherever and whenever the games have been played.
"When I take a team to St James' Park, I have stressed to the players that not only have they got to beat the opposition on the field, just as important is coping with the atmosphere created by the fans."
And rather than see them stay as a "wee club", the Scot admits he would prefer it if the Magpies could recapture the form they showed when they pushed United all the way in the 1995-96 season.
"The whole country would like to see a Newcastle team that matched the one in the Keegan era when they took us to the wire."
Sir Alex's original statement came after Chicharito (Javier Hernandez) gave his side an injury-time winner against Pardew's men at Old Trafford in December, with the Newcastle boss criticising his opposite number's treatment of the match officials.
He originally told reporters: "The problem for me and Manchester United is that the profile of the club is huge. I'm the manager of the biggest club in the world. I'm not like Newcastle, a wee club in the North-East."