I don't think PyPy is faster. Their design is significantly more complicated and thus takes longer to tune. Additionally I think python is a small bit more dynamic then Lua, complicating things.
I remember seeing a comparison between LuaJit and V8, both of which are highly tuned. LuaJit won on some of the benchmarks while V8 won others, and there were actually bit of a difference in the performance. That's the problem with Jitting, it's all tradeoffs. So what's good for a Jit in a browser is different from what's good in server environment. So you have to make a lot of benchmarks, testing widely different things, while at the same time not spending more time on optimizing one benchmark implementation in one language more than another.
I remember seeing a comparison between LuaJit and V8, both of which are highly tuned. LuaJit won on some of the benchmarks while V8 won others, and there were actually bit of a difference in the performance. That's the problem with Jitting, it's all tradeoffs. So what's good for a Jit in a browser is different from what's good in server environment. So you have to make a lot of benchmarks, testing widely different things, while at the same time not spending more time on optimizing one benchmark implementation in one language more than another.