Diffusivity calculations of argon and neon in are performed in carbon nanotubes (CNTs) with point defects mimicking those expected in real CNTs using equilibrium molecular simulation techniques. The Nose-Hoover NVT ensemble implemented in LAMMPS is used to perform equilibrium molecular dynamics simulations, and the uVT configurational-bias grand canonical Monte Carlo method implemented in Towhee is used to calculate the thermodynamic correction factor. The self-, corrected-, and transport diffusivities are calculated and compared to the values from pristine CNT calculations as well as the values suggested by experiment.