In our case we used a bus from Anuradhapura to reach Polonnaruwa. it was a slow trip in an old fashioned bus and as usual crowded. We even had a break down....!!!
Beware though to tell the driver to let you get off at Polonnaruwa "Old Town" close to Seylan Bank. The bus and train station are actually 3 kms away from there at the town of Kaduruwela. Neverthless the cost is very little!
Both the train and bus stations are in Kaduruwela, four kilometres east of town. Buses generally pass through town though so you should be able to hop off in the centre near the post office. You could hop on here as well when leaving, but if you want to make sure you have a seat you should go out to the bus station.
The best way to see the UNESCO site is by bike. Most people arrive and go through the site by car or large tourist bus. It's quite refreshing and cooling to ride through the gravel path by bike. You can rent the bikes at the rest house, by the Polonnaruwa museum. Also, you can pick up guides there -many have their own bikes.