The County Durham official sent off Orient midfielder Sean Thornton and gave Leeds an 80th-minute penalty and the anger of Orient manager Martin Ling was further increased when Miller and his assistants failed to spot that an 86th-minute shot from Boyd went over the goal line.
Ling insisted Miller had delivered a "biased" performance, but Boyd directed his criticism at Leeds after claiming that their bid to have the referee removed was a "deliberate attempt to influence Miller's judgment".
The request was made as a result of the confrontation between Miller and Wise at Southend United last season which earned Wise a fine from the Football Association.
But United's request to the Football League was rejected by the Professional Game Match Officials Board, which is responsible for the appointment of referees.
Boyd, who believed he had been denied a goal, said: "It was on Teletext about Dennis Wise having a go at him beforehand, and it worked. That's what he was trying to do, get him on side. I think he did it. Decisions went against us. There was no doubt in my mind that it was a goal."