Does n64 emulation run better than actual hardware?

No, compared to the actual hardware emulation can be horrible. Although there are many benefits from emulation such as modifications to the games, I prefer using an actual Nintendo 64 console as opposed to an emulator.

If your Nintendo 64 isn't running very well, it may need to be cleaned aswell as the contacts on the games.

With cartridge based consoles, they tend to pickup dust and anything else that may be in the air. I use an alcohol based solution and a cotton swab for cleaning my cartridges, many times blowing into them works.

:)