I'm a student, want to star some small Java projects, for fun and learning. I think GUI designer would be important, so guess NetBeans would be my choice. However, the company I'm working in and many many other people I know are using Eclipse. So...
IDEs and SDKs are not the same thing. Netbeans and Eclipse are IDEs (Integrated Development Environment). SDK is "Software development kit", basically, java, the compiler, and a whole bunch of other tools that you shouldn't worry about for now.
With the JDK alone, you can write java in a text editor and compile on the command line. IDEs are intended to simplify this process. Both Netbeans and Eclipse are powerful tools, but you're likely to be better off using what people around you are using so that you can learn from them.
I personally use Eclipse, but Netbeans is also very good. If you want to use the GUI designer, I would go with Netbeans because their GUI designer is much better. It is all preference. There is also products like JBuilder, Check out this page for a whole bunch of IDE's. http://www.webdeveloper.com/java/java_ides.html
Both Netbeans and Eclipse are good choices when it comes to java IDE, they both offer beginners a host of features and plugins that will make learning Java a lot easier. If you MUST HAVE a GUI designer then I would recommend netbeans (as its the only GUI designer I've actually tried) but for a beginner I recommend not using a designer all together. Especially just starting out learning how to design a GUI via code is useful. Java's windowing APIs are pretty simple to learn and shouldn't present too much of a challenge. My recommendation would be to just pick an IDE (either netbeans or eclipse) and start learning to code (don't worry about the GUI at first). Once you feel comfortable coding you can worry about GUI designers or not -- they're useful tools for rapid design but can also complicate the learning process.
I don't use GUI designers so won't comment on that aspect. Both are free so try each of them out. A lot of IDE choice boils down to personal preference, I'm a fan of text editors and command lines. No one can give you the "right" answer since no one is you and this is a fairly subjective area.
I'd say look for features that you are interested in and give all suitable IDEs a try. I'd been using eclipse for 5 years mostly because it was free and I liked in more than NetBeans. I just recently started using IntelliJ and like it a lot more but am paying the price for not having switched earlier.
Yes, if you like Netbeans, you should choose it over Eclipse. Choosing the IDE in which you more comfortable will help you learn Java and the tools much quicker. At a later date, it will probably be worthwhile to try Eclipse or IntelliJ. Each IDE has its strengths. I started with Netbeans and found it a much more initiative IDE than Eclipse. However, Eclipse is also an excellent IDE. Now I frequently use IntelliJ and Netbeans, and I kick around in Eclipse from time to time.