This may be an old question but I think it is still valid and the differences really depend on the type of lifestyle you are looking for. Not to mention that Nocatee has come a long way since 2007!
Ponte Vedra Beach offers a range of lifestyle choices from: Intracoastal, Oceanfront, Golf Course, Acreage as well as condos and townhouses. Prices range from 150K to multi-million dollar homes. Ponte Vedra Beach is known for its schools, gated communities and golf courses as well as the beach.
Nocatee students mostly attend the same schools as both Ponte Vedra Beach and Nocatee are in St Johns County. However Nocatee is currently building a new K-8 school. At its heart, Nocatee is about community living and the outdoors. Regardless of which community you live in, as a resident you are able to visit any dog park, the water park, playgrounds and added ball fields, not to mention the bike trails. New amenities are also being planned now to include kayaking, a pool, and gardening. They also have a monthly farmer's market and many community events.
One will not find beachfront or golf course views. Homes are more modestly priced between 150K - 600K depending on which community you are interested in. Some communities now only have resales while other communities are a mixture of new and resale homes. Nocatee was planned with long term vision so there are also more communities being introduced still.
While in 2007 it still seemed Nocatee was out of the way, construction of the 9B extension has helped to ease commutes. Currently the 5th best selling community in America, restaurants and retail chains won't be too far behind in dotting US 1 in the next few years.