Lee Ndlovu's brace and a header from James Armson secured the points.
"Naturally, I'm delighted with the three points," said Wilkin, whose side will end 2021 two points clear of second-place Gateshead.
"We had a close encounter at our place in the FA Trophy (a 2-1 defeat) and I felt we deserved a little more from that game."
Both camps were without players due to Covid, Gareth Dean and Wesley York missing from the Town side and Boston without Peter Crook, Scott Duxbury and Jake Wright jnr.
"We've come here today, Boston without crucial players and we're without crucial players," Wilkin added.
"But we've got on with it and the boys that have stepped in have done absolutely terrific.
"They (Dean and York) are big players and we don't have that much experience outside that (the first team squad), but we've asked the boys to step in at a difficult place against a very good side and they've stepped up to the plate."
Despite a dominant first half, the Saints didn't have things all their own way.
At 2-0 up Armson's penalty was saved by Marcus Dewhurst before United's Danny Elliott pulled one back from the spot.
The Pilgrims failed to turn chances into an equaliser, Ndlovu wrapping things up with his second in added time.
Wilin said: "I thought we were excellent first half and really limited Boston's chances.
"Second half, you know they're going to come out and there's a moment we miss our penalty and they score theirs. It tests your resolve a little bit.
"Probably the mosst pelasing thing is the boys have handled that bit of adversity, stayed strong together."