The closest either side came to scoring in the stalemate at Upton Park was when Cisse's first-half effort was cleared off the line by Winston Reid with Newcastle players and management staff feeling the ball had crossed the line before the defender's intervention.
McDonald hailed Reid for reacting to the chance and clearing what would have been a certain goal for Newcastle.
"If most of the ball is over the line it has to be all of it, but we thought from replays we saw it was not over the line," McDonald told Sky Sports.
"Sometimes you get them, sometimes you don't and I suppose Newcastle will be disappointed but we are pleased Winston Reid got back to clear the ball off the line and help keep a clean sheet."
McDonald admitted West Ham were disappointed not to take all three points after dominating the majority of the second half.
He added: "We are slightly disappointed we didn't score the first goal as I think it was always going to be a very, very tight game especially after the last two results Newcastle have had and they kept it nice and tight together and played dome decent football.
"We limited them to chances all the way through the game and we have come on strong towards the end and maybe could have nicked it late on.
"We hit the post and had a couple of other chances so we are slightly disappointed we didn't win the game."