Adam Marriott, Jordan Richards and Michael Gash found the net as the National League North leaders completed their first double over the Pilgrims since 1960.
Manager Elliott was left concerned by his side’s performance in the second half after they trailed 2-0.
“Ultimately, the biggest frustration is the reaction in the second half,” he said.
“It’s the first time I’ve seen a bit of adversity in the camp and I was interested to see how we came out of that.
“Too many leaders went hiding. Which is a concern, If I’m honest.
“I didn’t see it coming. I don’t want to come across disrespectful to King’s Lynn - they’re top of the league for as reason and you could see that today - but I just think the goals we conceded were poor and contributed a lot to them winning the game.
“I don’t want that to sound like I’m showing disrespect, but the levels we’ve been at, we were way below.
“I think there’s only Jake Wright who came out with any sort of credit in term of this performance.”
Marriott opened the scoring in the 28th minute as Boston appeared to be on top, with Richards firing home a long-distance effort just before the interval.
“Goals change games and the goal just before half time killed us,” Elliott said.
“I though the first goal was poor as there were no major threats really. Just one long ball in between the two centre backs, who I thought were poor today.”
Referencing Richards’ effort, he added: “The overwhelming one is in terms of how can a midfield player have time to take a touch 25 yards out and have a shot at goal? Our midfield players don’t get that.
“It’s not like us. I could hind behind fatigue but that’s just excuses.”
Gash was gifted a third after Peter Crook’s weak goal kick landed kindly to Marriott.
“It’s a difficult position and there have been a few goals over the past few weeks I think he could have done better with,” the manager continued.
“That last goal’s a massive error. The game was over as soon as he did that.
“I always try to work with my goalkeepers and let them have one error a month, that’s how I work it at this level.
“But now that’s too many.”
However, despite George Willis waiting in the wings, Elliott didn’t buy into speculation he could replace his number one, adding: “There’s no knee jerk reactions to anybody. Too many players went missing today.”