He was "joking" (probably actually testing Henry Hill to see how he'd react).

One of the most memorable moments from Goodfellas is Joe Pesci's "funny how" scene: https://youtu.be/yL9rSwrsMHw?si=8s3vkbr3n7dwh_yi Tommy could have been testing Henry. Tommy did bring to conclusion after the argument: "I almost had him!" There is something missing here. Anthony Stabile who tried to answer for Henry gave the clue in saying: "Tommy no, you got it all wrong." This was in case Tommy felt he was not laughing at the joke, but was making it personal instead. It is why Henry hesitated to let Tommy know how he actually felt. Tommy did feel offended when Henry called him a funny guy based on Joe Pesci's/Tommy DeVito's height of 5′4," thinking Henry was rather laughing at his short height, the way he talks and the whole little tough guy attitude. Tommy took it to heart, questioning Henry in what he thought was funny about him by asking questions of... Could it be the way he talks? Could it be that he's a little effed up? Could it be he is funny like a clown 🤡 in how he was amusing and making everyone laugh? and that he was at the restaurant to amuse people? LOL, it's already funny to think about it. As Tommy knew all eyes 👀 were on him for creating an argument, Tommy had to leave it in a good note and say he almost had Henry. But then when Sonny Bunz, the restaurant owner approached Tommy to tell him about an unpaid debt, he reacts aggressively and smashes a bottle on his head and kicks the bleeding owner across the room, bullies the waiter, all to the hysterical laughter of his friends. Henry furthermore tells Tommy: "You know what, you're a funny guy." Tommy pulls out his gun, thinking again, Henry is really effing with him by how he looks and talks after all.