Samuel Agba's early strike from spot at the Confluence Stadium saw the lead of the Peace Boys on the topflight log cut to two points with a victory for closer challengers, MFM.
Despite the defeat, the former Abia Warriors gaffer insists his side was better, describing the hosts as their weakest opponents of the season.
"It wasn't a bad game despite losing to Niger Tornadoes," Boboye told Goal.
"I will give kudos to my players because after a lot of frustration they gave a good account of themselves.
"This is one place we think of picking a point but I won't say much about the team because if this is how we play in the premiership then it’s a bad one and we are not learning.
"I'm disappointed because we came out to play If not for the frustration been giving us, we will have come out smoking than this.
"Not Niger Tornadoes, they didn't match our team (in terms of performance) and I think they are the weakest team I've played this season."