Both the technoligies have their own advantages. 

.Net
1) If the application is Windows platform specific then use .Net 
2) .Net is Language independent, so if the team has multiple skill expertise C#, VB.NET , C++ , developers can still work on the same project with different skill set. 
3) MS technologies provides RAD (rapid application development) to deviler project faster, customers always prefer faster delivery.
4) Debugging is very effort-less therefore, can fix the bugs quicker.
5) deployment is very easy and simple
6) Ajax implementation is simple & easy

.Java on the other hand
1) Platform independent
2) Open source
3) Dependant on the 3rd party tools to develop applications