depend on your mobo, some mobo provide software to control fan speed, eg Gigabyte Easytune, Asus got Qfan.

IF using stock heatsink, you can enable Intel speedstep or AMD cool and quite on mobo BIOS, and enable PWM Fan controlling so the stock fan will more quite at idle, you have to do this once only.
CnQ and speedstep no need to use software control, the software i mention above is for advanced controlling only.
If your case ventilation is poor and ambient temp is high, the fan will still spin faster anyway.

third party heatsink is your only option if you want more quieter since 3rd party hsf usually comes with large fan, and the heat dissipation is better than stock hsf.