id say thats your problem. your pc's specs arent great either. my freind had a pentium 3 with 16mb ram and he was able to play mario 64 at full speed but most of the other games were slow. you can speed things up a bit by disabiling sound with pj64.
also, tyy other emulators on your pc. nemu, 1964, mupen, corn or ultra hle.
some emulators can work better for you with your slow pc. corn is very fast on slow pc's but compatibilitys not great with it.
The bottleneck is the processor. The video card hardly has anything to do with emulation. Of course, there are a couple of optimizations that can be done. I am sure you would find them with a little searching.
Otherwise, you would try another emulator. 1964 has great compability and is faster than project 64. Mupen is also great, but slower.