There are private buses of Szwagropol from Krakow to Zakopane. They also stop in Nowy Targ. I think that it would be better option than public buses as private one are quite new and more comfortable. Probably cheaper, too. The price of normal ticket from Krakow to Nowy Targ is 11 zloty.
Nowy Targ as a capital of Podhale Region it has a Railway station. It is not big but all trains going from Krakow to Zakopane stops here. The trip takes about three hours but, compering to buses, you may enjoy your trip admiring beautiful views from the train... In addition, a trip by train is much comfortable. It is better to take a fast train - Express/IC (green colour) or pospieszny (red colour). Do not take osobowy trainas it is slow and stops at every stop.:)
Nowy Targ is easly reached by bus. There are more than 10 public buses of PPKS from Krakow to Nowy Targ. The trip sjould be not more than two hours. There is a big bus station in Nowy Targ (in the picture) where you can find some shops and kiosks with newspapers and magazines. The bus station is close to the city centre - about five minutes from the main market square. It is a good idea to travel by bus if you want to arrive to Nowy Targ in the centre.