In contrast to @John Fisher (+1) I'm a Java guy.
I am always jealous of the Windows/.Net world because everything seems to be much more integrated, at least for someone who is not familar with all the details and pitfalls.
The Java place is a bit more chaotic, therefore it produces a number of fairly innovative ideas (think of hadoop, Spring, etc.) outside of the JCP which promotes the official JavaSE and JavaEE standards. As the JCP is driven by a bunch of different (commercial) organizations it's sometimes far behind (e.g. lambda functions in Java) as it simply takes time to find agreements between all the different participants.
There are a number of pros and cons for both sides. Nevertheless, from a technical point of view it does not really matter whether to do Java or .Net as web development is much more about thinking in scalability and the overall complexity when it comes to e.g. 10k concurrent users accessing your system.
From a software architecture point of view .Net and Java (EE + frameworks) are fairly similar, they both provide APIs to solve all the common problems (e.g. MVC, Rest, JSON, Persistence, messaging - just to name a few) we're facing in today's world.
To conclude - have a look at both concepts and pick one. It's not a decision for lifetime.