Eclipse is a pig unless you have some a very solid desktop IME. I haven't touched Java in ages, but check out Introduction to Java Programming by YD Liang as well (+1200 pages, very thorough and a nice wide scope). There's another book called Learn Java for Android Development which is meant to be a quick introduction so you can move on to doing Android.
+1 for Netbeans, it's a great IDE for *nix related languages.
I have been developing in Java since - what? - 1998 or so?
Ok - so there are a few things I would recommend.
So for a beginners book; Bruce Eckel is a good author. Thinking in Java, 4th Edition, is a little dated but probably still a solid book.
Herbert Schildt is another good author. Java, A Beginner's Guide, 5th Edition would be another good book.
A different format from the rest, is the Head First Java. This uses more pictures, with the idea that some of us are very visual. Others do not care for that style, feeling like it's more like a comic book. I say give it a look and see if you like it. Finally, there is The Java Tutorial: A Short Course on the Basics, 4th Edition.
I also recommend a solid foundation in Object Oriented Design, since Java is an Object Oriented language. Head First Object Oriented design and Analysis is a great book; one of the better head first books. There are other in this category as well.
Finally, there is a web site full of info and geared towards beginning Java developers; http://www.javaranch.com/
I would like to comment on Eclipse; the latest version, Juno, really does seem to be slow. I recommend using the previous version; Indigo, until they get bugs worked out.