Likely. Pennywise had a few major weaknesses: arrogance, limitations of the form it took, and the conviction of its enemies. In the book, the kids were able to overcome It, because they believed they could. I doubt Joker's convictions would be less than a bunch of scared kids. I should also add that Joker obviously wouldn't be dealing with the pants-shitting terror that the kids dealt with.
The only real problem is if Pennywise knows about Joker and his characteristics. Pennywise played around with kids, because he didn't think they were anything to worry about. If he for any reason thought Joker could be a threat, he might just go for a quick kill. In that case, Joker could be in a lot of trouble.