Alex Nicholls continued his recent run of good form by putting Northampton in the lead but home side Argyle roared back with three second half goals, David Artell's late consolation unable to prevent a first league defeat of the season for Town.
"You see what an organised and good side Northampton are," Fletcher told BBC Radio Devon.
"And they're going to be there or thereabouts come the end of the season so it's a good win for us today."
Boothroyd blamed a 'lacklustre' opening to the second period for his side's downfall as they conceded three goals for the third consecutive game.
"The three goals we have conceded were all very poor goals," he said.
"We hit the post and we scored one late on and on another day we would have won that game 5-3 or 6-3 but at the same time we could’ve lost 7-6.
"So we played our part in a spectacle but we want to be winning spectacles like this."
Town now turn their attention to Tuesday night's JPT tie against MK Dons at Sixfields.