The midfielder scored what proved to be the decisive goal from the penalty spot in their 3-1 victory at Kilmarnock after John McGinn's opener had been cancelled out by Kris Boyd.
On-loan Newcastle midfielder Conor Newton then scored the final goal two minutes from time but talks have now stalled on a new deal for McGowan to leave Lennon frustrated.
"It's still in the balance. I haven't had a conversation with the boy for a number of weeks now," said Lennon.
"I opened up talks with him about three months ago and he knows where we stand. I know exactly what his intentions are but we can't wait for ever."
Lennon is more upbeat about his chances of taking Newton and team-mate Paul Dummett back on loan again next season, however.
"The two of them are good players and the boy Dummett just loves defending," added Lennon.
"He's been a pleasure to have. Our club now has a reputation now of bringing in players and improving them.
"Newcastle have got to welcome the boys back but we have a very good relationship with them. If they are going to go back out anywhere then I dare say we are in with a good shout."
Lennon also handed debuts to youngsters AntonBrady, who was fouled for the penalty award, as well as Mo Yaqub and Jack Smith and he was delighted at their progress.
"It was fantastic that we managed to get another three young boys on at the end and we had seven players under the age of 20 featuring too," said Lennon.
"Credit too to the young lads Killie had out and that's a great advert for Scottish football there.
"We will have to carry a balance of young players next season and these young kids, Jack, Anton - who did well to win the penalty - and Mo have been exceptional at reserve level.
"A great deal of credit must also go to our head of youth David Longwell and his assistant Frazer Robertson for these wee diamonds they are bringing up to us and it's now up to me to polish them."