PyPy mostly cares about large scale programs (thanks to a large quantity of Python libraries it's not that hard), while LuaJIT usually cares for smaller stuff.
Last time I tried to run richards (which is the largest example I found for both Lua and Python), PyPy was able to eventually outperform LuaJIT slightly, given enough iterations, however LuaJIT warmup time was very very impressive and it was much faster at the beginning.
From a very unscientific perspective I would expect LuaJIT to mostly outperform PyPy, especially on stuff where it's feasible to compare, like by implementing small numeric kernels in both Lua and Python, but I haven't measured a whole lot in this area. LuaJIT definitely outperforms PyPy on the computer language shootout benchmarks. I would also expect the field to be more leveled if you implement say a webserver in both, caring about performance, but this is really on the guessing side.