In Punta del Este, the best restaurants are located in Jose Ignacio. La Huella is a delicious seaside restaurant right on the beach - excellent drinks, sushi and fresh seafood. http://www.paradorlahuella.com/
Also there is Namm and Marismo are excellent, both off the beaten path in the woods (literally) - to go there is an experience in itself. Both restaurants are very popular in the high season (Dec - Feb) so have your hotel make reservations for you.
I've never stayed in Punta proper, only in La Barra, which I would highly recommend over downtown Punta. Good hotel choices are Le Club and La Posta del Cangrejo. La Posada del Faro and Azul Marino are also nice in Jose Ignacio.
Have a great time, Uruguay is beautiful!