This is where the whole "novel legal theory" comes in. You're correct that the charge of falsifying business records is a misdemeanor. However, if done to cover up a previous crime, it becomes a felony with a longer statute of limitations. That's exactly what the prosecutors did here. They alleged Trump falsified the records to hide another crime, but never specified the other crime.
“They alleged Trump falsified the records to hide another crime, but never specified the other crime”
According to NY law, they don’t have to prove beyond a reasonable doubt that the other crime happened. Using Cohen’s, Pecker’s and some other testimony, they were able to convince the jury the other crime likely happened