Andy Carroll fired the visitors in front with a superb left-footed strike shortly before half-time at the Liberty Stadium, but a Mark Noble own goal earned Swansea a share of the spoils 16 minutes from time.
McDonald - standing in for the unwell Sam Allardyce - believes West Ham did enough to pick up maximum points.
"I think we should have won it," he said. "We created some really good chances, Andy scored a fantastic goal to set us up and we kept Swansea at arm's length.
"They were shooting from distance, never really got through us, never really got behind us, and when they did, we put our bodies on the line."
Allardyce sent his team to South Wales with a new formation - starting with three at the back, flanked by two wing-backs - and McDonald was happy with how the system panned out.
"We do practice different formations," he continued. "We knew Swansea would have the ball, they've got some really good movement, so we just tried to stifle the space that they had.
"That worked a treat, so that was great.
"We've got the energy of the two wing-backs [Carl Jenkinson and Aaron Cresswell] to try and get forward and we've got lots of people on the ball in midfield who can pass and move, so I thought the tactics worked really well."
Noble's own goal came when he failed to clear off the line from a Bafetimbi Gomis header, but McDonald sympathised with the experienced midfielder.
"Mark's come into the team the last two games and acquitted himself really well," he remarked. "He keeps the ball moving, he sets the tempo for us, and nine times out of 10 he does clear that off the line.
"It's taken a nick off the post and a little ricochet, which sometimes you can't do too much about."
Discussing Allardyce's absence, McDonald added: "He's got a chest infection. He was watching the game on the computer and he was giving us a few little tips on the phone just to try and point us in the right direction.
"He's taken time off to recover and I'm sure he'll be fine for next week."
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