Go with AANAC. Both AANAC and NRAI require that you complete a course to get the certification, but only AANAC gives you a choice of doing them online. NRAI requires that you sit through their course, which is only offered a couple of times during the year. AANAC can be done anytime online. It is the more respected of the two, and I'm thinking it's also cheaper. As far as MDS 3.0 goes, you will still be working with MDS 2.0 for another fifteen months before 3.0 goes into effect. AANAC will have a 3.0 course available when the time comes.
Also check out
www.mdstraining.org, which is a free online MDS tutorial from CMS. Good luck.