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Manager Brian Laws said: "It's a bad ending to the year and we must hope for a better start in the New Year.
"Today has summed up a topsy-turvey year. We have been very up and down and we need to change quickly if we are to get into the play-offs.
"We were intimidated by Boston but give them credit for that. They are only an average third division side and we have to beat them if we are to progress.
"You have got to ask the questions of the players, I'm not kicking the ball for them.
"If they are not kicking the ball to each other you have got to ask them questions, (especially) the younger players because it is the younger players who were abysmal today.
"They are a young side but we have to work like that because of the finances.
"At the moment I can't have a go at the forwards because they're not getting the service."
Right-back Nathan Stanton was replaced by Wayne Graves, once again asked to fill-in at right back, but Laws expects him to be fit for the trip to Second Division Barnsley in the FA Cup next week.
He added: "He got a kick on the ankle and his whole foot went numb, we think he hit a nerve.
"He is on crutches at the moment, I'm sure that it will clear up in the next 24 hours."
Boston boss Neil Thompson was upbeat with his side's second away win of the campaign.
He said: "We battled well and ran our socks off, it was a typically tight local derby and I thought we deserved the three points.
"We had a system in hand to deal with the Scunthorpe strike force of Torpey, MacLean and Hayes and it worked very well.
"We were very committed and the players proved themselves excellently."