The choice is yours, but there are some considerations for each;

Plastic bottles are fine if you are planning on drinking your beers over a short period of time, however, after several months, plastic bottles can start to leak CO2 and the beer may become flat. Remember PET bottles have a maximum re-use limit too, as the bottles become weaker over time with the CO2 pressure building up during carbonation.

Glass bottles with caps are good and are what most commercial breweries use. They will keep for a long time and should not lose any CO2. They are far more reusable than plastic. 

Preference is brown or at least green is better than clear. Even being careful to keep the bottles out of direct light will seriously reduce the expiry of the beer.

Flip-top bottles have the added benefit of not having to cap the beer and also beer can be saved for a couple of days after original opening without going flat. Plus, flip-top bottles are reusable and look really cool!