The big Eclipse git plugin is egit, which is now an official Eclipse subproject -- http://www.eclipse.org/egit/
. I've been using NetBeans lately but I was checking out egit last week, and at first glance it seemed a lot nicer and more mature than the NetBeans git plugin.
I'll second what Tim said. I'm using a similar setup with NetBeans. I've got the NetBeans git plugin (nbgit) installed, but I only use it to do the equivalent of "git status" and "git diff". For all the other operations (merging, branching, history, remote repositories), I switch over to the command line. NetBeans is fine with this; I just have to remind it to refresh its git status occasionally.
Having used CVS and SVN extensively in Eclipse in the past, I found that it was a little tricky adjusting to git in Eclipse. It was actually a pretty similar experience to when I first started using git at the command-line, just figuring out the different workflow that comes from the basic conceptual differences between the systems.
I'll also add that, when I switched from SVN to git about six months ago, I found that I could scrape out a bare bones basic workflow with "cheat sheets" and some instruction from my co-workers, but I had no idea what the commands were really doing until I spent several hours reading the O'Reilly git book.