Dear Ms. Lu,
Thanks for contacting Top China Travel!
Both way are fine and convenient to go to Zhujiajiao Water Town from Shanghai. You may choose the one that is near to your hotel.
Both of them takes about 1.5 hours. I am not sure about the price. But it shall not be more than RMB 15 for one way.
Any further request or question, please feel free to contact with us.