Call me a n00b but I didn't really got those1) Determine the bottleneck if turning on the real time statistics in your emulator. Both 1964 and PJ64 support such a thing. Your emulator will then show the CPU percentage usages on the status bar.
Most CPU should be used by video plugin and emlator r4300i core.
2) Using higher speed counter if the r4300i is using the most CPU power. Almost all emulators are supporting counter speed change. For 1964, you can use 4 or 5 instead of the default value 2.